My clutch pedal squeaks on its way in and out. I was hoping it was the pedal itself, but when I got under the car it sounded like it's coming from under the engine, where I presume the clutch is located.
The car is a 2003 Civic sedan.
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The squeak.. if not from the pedal, cable or clutch slave cylinder is likely from either the clutch cover fingers or release bearing/return spring. Whilst the squeak itself is not likely a serious issue. If the clutch has been installed for a long time it could be a sign that it is becoming worn and the squeaking perhaps down to the amount of clutch dust in the bell housing/clutch casing. If the clutch is working well though, no slipping or stiffness in the pedal operation etc, I would just monitor the squeak.. If it becomes more noticeable or changes in some way then its time to have mechanism/clutch inspected.
In my case (different car, though), the culprit was the clutch fork rubbing against a nearby metal part, probably the casing. (Clutch fork is the lever sticking out of the gearbox which is pushed by the clutch slave cylinder).
After I removed the clutch fork boot and sprayed some lubricant inside, the clutch pedal became silent and easier operated, too.
You may find this video useful.