My 4Runner’s clutch pedal makes a strange clicking noise when I’m pressing and depressing it, like a clicking/popping noise that I can almost feel with my foot if I press it down slowly enough. It doesn’t seem to be anything in the transmission, it sounds like it’s coming from the inside of the car. I sprayed the moving bits around the pedal and the bushing with silicone spray and that didn’t do anything. Coworker of mine determined it’s likely the master cylinder, though I don’t currently have any other symptoms relating to that and would like to further troubleshoot before I go replacing parts.

Any tips or advice would definitely be appreciated!

 

The bracket is known to crack. Take a close look as it may be the source of your noise.

 

Yes. Mine failed from metal fatigue at 163,000. Search on this site for posts on DIY repair. Need welding eqpt and skills. I had mine done at a shop, new bracket, along with the shifter bushing and seat replacement.. $463 14 years ago. I think I read somewhere that not having your foot squarely on the pedal when you push it in can hasten the failure.

 

I dunno about foot placement. We started replacing them fairly early on. Didn’t seem as robust as they maybe should have been.

 

Mine actually wore out the hole where the master mounts to the pedal and made a creaking sound. Was able to buy a new pedal and replaced all the bushings/regreased the spring while I had it all out. So there's a few issues it could be.

Short list:
Worn spring bushings
Cracks somewhere in the linkage/pedal
Worn hole (ha) where the master mounts to the pedal

 

Check to see if it's the proximity switch making the noise, or the interface with it.