2016 YAMAHA WR 250F check engine

IGNITION SYSTEM
9-4
EAS2GB7359TROUBLESHOOTING
The ignition system fails to operate (no spark or intermittent spark).
TIP
Before troubleshooting, remove the following part (s):
1. Seat
2. Side cover (left/right)
3. Air scoop (left/right)
4. Fuel tank
5. Fuel tank
1. Check the fuse.
Refer to “CHECKING THE FUSES”
on page 9-68.NG 
Replace the fuse(s).
OK 
2. Check the battery.
Refer to “CHECKING AND
CHARGING THE BATTERY” on
page 9-69.NG 
• Clean the battery terminals.
• Recharge or replace the battery.
OK 
3. Check the spark plug.
Refer to “CHECKING THE FUSES”
on page 9-68.NG 
Re-gap or replace the spark plug.
OK 
4. Check the ignition spark gap.
Refer to “CHECKING THE IGNI-
TION SPARK GAP” on page 9-73.OK 
The ignition system is normal.
NG 
5. Check the ignition coil.
Refer to “CHECKING THE IGNI-
TION COIL” on page 9-74.NG 
Replace the ignition coil.
OK 
6. Check the crankshaft position sen-
sor.
Refer to “CHECKING THE CRANK-
SHAFT POSITION SENSOR” on
page 9-74.NG 
Replace the stator assembly.
OK 
7. Check the engine stop switch.
Refer to “CHECKING THE
SWITCHES” on page 9-64.NG 
Replace the engine stop switch.
OK 

ELECTRIC STARTING SYSTEM
9-11
8. Check the main relay.
Refer to “CHECKING THE RE-
LAYS” on page 9-72.NG 
Replace the main relay.
OK 
9. Check the neutral switch.
Refer to “CHECKING THE
SWITCHES” on page 9-64.NG 
Replace the neutral switch.
OK 
10.Check the clutch switch.
Refer to “CHECKING THE
SWITCHES” on page 9-64.NG 
Replace the clutch switch.
OK 
11.Check the engine stop switch.
Refer to “CHECKING THE
SWITCHES” on page 9-64.NG 
Replace the start switch.
OK 
12.Check the start switch.
Refer to “CHECKING THE
SWITCHES” on page 9-64.NG 
Replace the engine stop switch.
OK 
13.Check the entire starting system’s
wiring.
Refer to “CIRCUIT DIAGRAM” on
page 9-6.NG 
Properly connect or repair the starting sys-
tem’s wiring.
OK 
Replace the ECU.

FUEL INJECTION SYSTEM
9-30
EAS2GB7374ECU SELF-DIAGNOSTIC FUNCTION
The ECU is equipped with a self-diagnostic function in order to ensure that the fuel injection system
is operating normally. If this function detects a malfunction in the system, it immediately operates the
engine under substitute characteristics and illuminates the engine trouble warning light to alert the
rider that a malfunction has occurred in the system. Once a malfunction has been detected, a fault
code number is stored in the memory of the ECU.
• To inform the rider that the fuel injection system is not functioning, the engine trouble warning light
flashes while the start switch is being pushed to start the engine.
• If a malfunction is detected in the system by the self-diagnostic function, the ECU provides an ap-
propriate substitute characteristic operation, and alerts the rider of the detected malfunction by illu-
minating the engine trouble warning light.
Engine trouble warning light indication and fuel injection system operation
* The warning light flashes when any one of the following conditions is present and the start switch
is pushed:
Checking the engine trouble warning light
The engine trouble warning light comes on for around 2 seconds when pushing the start switch to
turn on the meter light and the engine trouble warning light comes on while the start switch is being
pushed.Warning light indica-
tionECU operationFuel injection opera-
tionVehicle operation
Flashing* Warning provided
when unable to start
engineOperation stopped Cannot be operated
Remains on Malfunction detected Operated with substi-
tute characteristics in
accordance with the
description of the mal-
functionCan or cannot be oper-
ated depending on the
fault code
12: Crankshaft position sensor 41: Lean angle sensor
(open or short circuit)
30: Lean angle sensor
(latch up detected)50: ECU internal malfunction
(faulty ECU memory)
33: Ignition coil
(Malfunction detected in the primary wire
of the ignition coil)
a. The meter light does not come on.
b. The meter light comes on.
c. Light OFF
d. Light ON for 2 seconds
ab
cdc

FUEL INJECTION SYSTEM
9-31
ECU detects an abnormal signal from a sensor
If the ECU detects an abnormal signal from a sensor while the vehicle is being driven, the ECU illu-
minates the engine trouble warning light and provides the engine with alternate operating instructions
that are appropriate for the type of malfunction.
When an abnormal signal is received from a sensor, the ECU processes the specified values that are
programmed for each sensor in order to provide the engine with alternate operating instructions that
enable the engine to continue operating or stop operating, depending on the conditions.
EAS2GB7375TROUBLESHOOTING METHOD
The engine operation is not normal and the engine trouble warning light comes on.
1. Check:
• Fault code number
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a. Connect the Yamaha diagnostic tool. Refer to “YAMAHA DIAGNOSTIC TOOL” on page 9-32.
b. Check the fault code number displayed on the Yamaha diagnostic tool.
c. Identify the faulty system with the fault code number.
d. Identify the probable cause of the malfunction.
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2. Check and repair the probable cause of the malfunction.
3. Perform the reinstatement action for the fuel injection system. Refer to “Confirmation of service
completion” in the appropriate table in “TROUBLESHOOTING DETAILS” on page 9-35.
4. After pushing the engine stop switch, push the start switch to check whether the fault code no. is
displayed.
TIP
If another fault code number is displayed, repeat steps (1) to (4) until no fault code number is dis-
played.
5. Erase the malfunction history in the diagnostic mode. Refer to “SENSOR OPERATION TABLE”
(Diagnostic code No.62).
TIP
Turning off the meter light will not erase the malfunction history.
The engine operation is not normal, but the engine trouble warning light does not come on.
1. Check the operation of the following sensors and actuators in the diagnostic mode. Refer to
“TROUBLESHOOTING DETAILS” on page 9-35.
If a malfunction is detected in the sensors or actuators, repair or replace all faulty parts.
If no malfunction is detected in the sensors and actuators, check and repair the inner parts of the
engine.Fault code No. No fault code No.
Check and repair. Refer to “TROUBLESHOOT-
ING DETAILS” on page 9-35.
Monitor the operation of the sensors and actua-
tors in the diagnostic mode. Refer to “TROU-
BLESHOOTING DETAILS” on page 9-35 and
“LIST OF SELF-DIAGNOSTIC AND FAIL-SAFE
ACTIONS” on page 10-5.Check and repair.
01: Throttle position sensor signal (throttle angle)
30: Ignition coil
36: Injector

FUEL INJECTION SYSTEM
9-35
6. Condition
The current conditions are displayed. (Detected/Recovered)
7. Symptom
The symptoms of the detected malfunction are displayed.
8. Diagnosis code
The diagnosis codes related to the detected malfunction are displayed.
9. FFD (only for models that can display freeze frame data)
The mark “ ” is displayed when the freeze frame data is available.
10.ECU conduction time (hour: minute: second)
The total ECU conduction time (total hours the vehicle’s start switch was ON) when the malfunc-
tion was detected is displayed.
11.Number of main switch operation after detection
The number of times the meter light comes on by pushing the start switch between the malfunction
detection and code reading is displayed.
12.Number of occurrences
The number of malfunction occurrences between the malfunction detection and code reading is
displayed.
EAS2GB7377TROUBLESHOOTING DETAILS
This section describes the measures per fault code number displayed on the diagnostic tool. Check
and service the items or components that are the probable cause of the malfunction following the or-
der given.
After the check and service of the malfunctioning part have been completed, reset the diagnostic tool
display according to the reinstatement method.
Fault code No.:
Fault code number displayed on the diagnostic tool when the engine failed to work normally.
Diagnostic code No.:
Diagnostic code number to be used when the diagnostic mode is operated.
Fault code No. 12
ItemCrankshaft position sensor: no normal signals are received
from the crankshaft position sensor.
Fail-safe systemUnable to start engine
Unable to drive vehicle
Diagnostic code No.—
Diagnostic tool display—
Procedure—
ItemProbable cause of malfunc-
tion and checkMaintenance jobConfirmation of service
completion
1 Connection of crankshaft po-
sition sensor coupler.
Check the locking condition
of the coupler.
Disconnect the coupler and
check the pins (bent or bro-
ken terminals and locking
condition of the pins).Improperly connected 
Connect the coupler securely
or repair/replace the wire har-
ness.Crank the engine.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 2.

FUEL INJECTION SYSTEM
9-36
2 Connection of wire harness
ECU coupler.
Check the locking condition
of the coupler.
Disconnect the coupler and
check the pins (bent or bro-
ken terminals and locking
condition of the pins).Improperly connected 
Connect the coupler securely
or repair/replace the wire har-
ness.Crank the engine.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 3.
3 Wire harness continuity. Open or short circuit  Re-
place the wire harness.
Between the crankshaft posi-
tion sensor coupler and ECU
coupler.
black/blue–black/blue
gray–grayCrank the engine.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 4.
4 Installed condition of crank-
shaft position sensor.
Check for looseness or
pinching.
Check the gap between the
crankshaft position sensor
and the pickup rotor.Improperly installed sensor
 Reinstall or replace the
sensor.
Refer to “GENERATOR AND
STARTER CLUTCH” on
page 6-62.Crank the engine.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 5.
5 Defective crankshaft position
sensor.Check the crankshaft position
sensor.
Refer to “CHECKING THE
CRANKSHAFT POSITION
SENSOR” on page 9-74.Crank the engine.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 6.
6 Malfunction in ECU. Replace the ECU. Fault code No. 12
ItemCrankshaft position sensor: no normal signals are received
from the crankshaft position sensor.

FUEL INJECTION SYSTEM
9-37
TIP
• If fault code Nos. 13 and 14 are both displayed, perform the checks and maintenance jobs for fault
code No. 13 first.
• Before troubleshooting, disconnect the starter motor lead from the starter relay.
Fault code No. 13
Item Intake air pressure sensor: open or short circuit detected.
Fail-safe systemAble to start engine
Able to drive vehicle
Diagnostic code No.03
Diagnostic tool displayDisplays the intake air pressure.
ProcedureOperate the throttle while pushing the start switch.(If the display
value changes, the performance is OK.)
ItemProbable cause of malfunc-
tion and checkMaintenance jobConfirmation of service
completion
1 Connection of intake air pres-
sure sensor coupler.
Check the locking condition
of the coupler.
Disconnect the coupler and
check the pins (bent or bro-
ken terminals and locking
condition of the pins).Improperly connected 
Connect the coupler securely
or repair/replace the wire har-
ness.Push the start switch.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 2.
2 Connection of wire harness
ECU coupler.
Check the locking condition
of the coupler.
Disconnect the coupler and
check the pins (bent or bro-
ken terminals and locking
condition of the pins).Improperly connected 
Connect the coupler securely
or repair/replace the wire har-
ness.Push the start switch.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 3.
3 Wire harness continuity. Open or short circuit  Re-
place the wire harness.
Between intake air pressure
sensor coupler and ECU cou-
pler.
black/blue–black/blue
pink–pink
blue–bluePush the start switch.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 4.
4 Installed condition of intake
air pressure sensor.
Check for looseness or
pinching.Improperly installed sensor
 Reinstall or replace the
sensor.Push the start switch.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 5.

FUEL INJECTION SYSTEM
9-38
TIP
• If fault code Nos. 13 and 14 are both displayed, perform the checks and maintenance jobs for fault
code No. 13 first.
• Before troubleshooting, disconnect the starter motor lead from the starter relay. 5 Defective intake air pressure
sensor.Execute the diagnostic mode.
(Code No. 03)
When engine is stopped:
Atmospheric pressure at the
current altitude and weather
conditions is indicated.
At sea level: Approx. 101 kPa
1000 m above sea level: Ap-
prox. 90 kPa
2000 m above sea level: Ap-
prox. 80 kPa
3000 m above sea level: Ap-
prox. 70 kPa
When engine is cranking:
Make sure that the indication
value changes.
The value does not change
when engine is cranking. 
Check the intake air pressure
sensor.
Replace if defective.
Refer to “CHECKING THE
INTAKE AIR PRESSURE
SENSOR” on page 9-80.Push the start switch.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 6.
6 Malfunction in ECU. Replace the ECU.
Fault code No. 14
ItemIntake air pressure sensor: hose system malfunction (clogged
or detached hose).
Fail-safe systemAble to start engine
Able to drive vehicle
Diagnostic code No.03
Diagnostic tool displayDisplays the intake air pressure.
ProcedureOperate the throttle while pushing the start switch.(If the display
value changes, the performance is OK.)
ItemProbable cause of malfunc-
tion and checkMaintenance jobConfirmation of service
completion
1 The intake air pressure sen-
sor hose is damaged, discon-
nected, clogged, twisted or
bent.Repair or replace the sensor
hose.Start the engine and let it idle
for approximately 5 seconds.
Fault code number is not dis-
played  Service is finished.
Fault code number is dis-
played  Go to item 2. Fault code No. 13
Item Intake air pressure sensor: open or short circuit detected.