Mercury 40 HP 2 Stroke Problems: 5 Major Issues

Despite being so popular around the world, Mercury 40 HP 2 stroke problems are so common that most boat owners face. While this engine is known for its reliability and performance, some problems usually arise over time. 

In this article, I will discuss the most frequent Mercury 40 HP 2 Stroke Problems and provide insights into their symptoms, reasons, and solutions. So, if you have a boat with this engine, please read on.

Mercury 40 HP 2 Stroke Problems and Solutions At a Glance

Before we head toward the main part to discuss the problems and solutions, let’s check out a quick overview of them.

Engine Dies After Running for a Few SecondsCheck and clean or replace fuel filters and lines regularly
Defective Diaphragm PumpRegularly inspect and clean the diaphragm pump
The Motor Slows Down to About Half of the SpeedInspect and clean or replace spark plugs
Sounds Like the Idle JetClean the idle jet thoroughly
Upper Cylinder Is Not FiringCheck and replace any faulty spark plugs or ignition coils

If you have some time, please check a comprehensive guide on Mercury 75hp 2 Stroke Problems, that I covered a few days back.

Problem 1: Engine Dies After Running for a Few Seconds

One of the most frustrating problems with the Mercury 40 HP 2-stroke is when the engine suddenly shuts down after starting and running for just a few seconds.


  • The engine starts successfully but then stalls quickly.
  • There may be difficulty in restarting the engine after it stalls.
  • This issue is more likely to occur when the engine is cold.


  • Clogged fuel filters or lines can restrict the flow of fuel to the engine.
  • Malfunctioning spark plugs may lead to incomplete combustion.
  • Ignition system problems, such as faulty ignition coils or a malfunctioning kill switch, can cause sudden engine shutdowns.


  • Check and clean or replace the fuel filters and lines regularly.
  • Inspect and replace spark plugs as needed, following the manufacturer’s recommendations.
  • Verify the ignition system components for any defects and have them repaired or replaced if necessary.

Problem 2: Defective Diaphragm Pump

The diaphragm pump in the Mercury 40 HP 2-stroke outboard motor plays a crucial role in delivering fuel to the engine. When this pump malfunctions, it can lead to significant performance issues.


  • The engine sputters or stalls during acceleration.
  • Poor fuel efficiency and increased fuel consumption.
  • Difficulty starting the engine.


  • A worn-out or torn diaphragm can cause fuel leaks, leading to an improper fuel-air mixture.
  • Contaminants in the fuel can damage the diaphragm and hinder its proper operation.
  • Improper maintenance and lack of regular inspection can contribute to diaphragm pump failure.


  • Regularly inspect and clean the diaphragm pump for any signs of damage or wear.
  • Use high-quality, clean fuel to prevent contamination issues.
  • Replace the diaphragm pump if it is damaged or not functioning correctly.

Problem 3: Motor Slows Down to About Half Speed

Observing a significant decrease in engine speed while running can be a concerning problem, affecting the overall performance of the boat.


  • The engine struggles to reach its full RPM range.
  • Reduced power output, leading to slower acceleration and overall speed.
  • The boat may not plan properly due to the lack of sufficient power.


  • Spark plug fouling or ignition system issues can result in incomplete combustion.
  • Fuel delivery problems, such as clogged jets or carburetor issues, can limit the engine’s power output.
  • Excessive carbon buildup on engine components can impede the proper functioning of the motor.


  • Inspect and clean or replace the spark plugs to ensure a strong spark and complete combustion.
  • Clean the carburetor and fuel jets to improve fuel delivery to the engine.
  • Regularly use fuel additives to prevent carbon buildup in the engine.

Problem 4: Sounds Like the Idle Jet

Unusual sounds coming from the engine, such as a high-pitched whistling or buzzing noise, can be a sign of trouble with the idle jet.


  • The engine may idle roughly or stall when idling.
  • The unusual sound becomes more pronounced when the engine is idling.
  • There might be fluctuations in the idle speed.


  • The idle jet may be partially clogged or blocked, affecting fuel flow during idle conditions.
  • Fuel quality issues or water contamination in the fuel can lead to idle jet problems.
  • Poor maintenance and lack of regular servicing can contribute to idle jet-related issues.


  • Clean the idle jet thoroughly to ensure smooth fuel flow during idling.
  • Use high-quality, clean fuel to prevent fuel-related problems.
  • Adhere to the recommended maintenance schedule and service the engine regularly.

Problem 5: Upper Cylinder Is Not Firing

If one of the cylinders in the Mercury 40 HP 2-stroke engine fails to fire, it can cause a severe drop in engine performance.


  • Noticeable loss of power and reduced acceleration.
  • The engine misfires and runs unevenly.
  • Increased exhaust emissions and possible overheating.


  • A faulty spark plug or ignition coil can cause a particular cylinder to misfire.
  • Compression issues, such as a damaged cylinder head gasket, can lead to poor cylinder firing.
  • Carbon deposits or debris in the cylinder can hinder proper combustion.


  • Check and replace any faulty spark plugs or ignition coils.
  • Perform a compression test to identify and address any compression-related problems.
  • Regularly clean and maintain the engine to prevent carbon buildup.
  • Conclusion

I think you’re now clear about the Mercury 40 HP 2 Stroke Problems. Now, before you go, please check out another guide on Mercury 75 hp 2 Stroke Carburetor Adjustment.

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