My wife is the main driver of our 99 and this last week it has started to get really cold at night, she mentioned to me over the weekend that the brakes are really bad when she goes out to work in the morning. I got in it the next morning and sure enough, the pedal is completely dead until it's basically on the floor and then the brakes will grab. Drove it around for a few minutes and the brakes came back to normal, basically as the engine came up to operating temps.
Gave her my truck for work this morning so I could check it out again, and sure enough for the first 5-10 minutes of driving they were dead.
Any suggestions on where the issue could be? I've been meaning to get the brakes done anyway so I ordered new pads, rotors and stainless brake lines to do this weekend, will flush with new fluid as well. I know the pads and rotors aren't going to really fix this issue but thought the fluid could possibly be really old, I've only had the 4runner since around April this year.
I have searched a bit but haven't seen any thread with the same issue as mine.

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First question I have is how long has it been since brake fluid change and brakes bled?
Brake fluid gathers moisture as it ages - could be freezing in system.
If air is in system it takes up less space when cold - pedal to floor till things warm up.
How does pedal feel when you get it back?

I'm not sure, I've had the 4Runner for around 6months so not sure about all that. I have parts on the way to do the brakes and will do a fluid flush at the same time.
The brakes feel fine when the weather is warmer, only happens when it sits overnight with this cold weather.
The fluid was going to be my first thing to try, just was wanting to see if anyone has seen the same issue.

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Sounds very much like air in the brake lines and the lines need to be bled. Only replace the pads if they are worn, no need to otherwise.

Last weekend I installed new rotors, pads and hardware, wheeler off-road SS brake lines and did just enough of a bleed to get air out from the new lines. The fluid was discusting but I didn't have time to flush much.
The brakes felt much better but still had intermittent soft and long travel in the pedal.
Today I did a full flush until clean fluid was coming from each bleeder valve. Now the pedal is feeling really nice and the stopping power is better than I've ever felt in the 4runner. I was able to get ABS to kick on when doing hard stops from about 40-50 mph. Never kicked in before.

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