As others have said, there is no sharp boundary for the atmosphere, but for Earth we have defined the Karman line, where a plane would have to be traveling at orbital velocity for its wings to provide enough lift to support itself. Even this value is not precise (air pressure can vary, for instance), but two widely-used values are 50 miles (about 80 km) and 100 km.
Interestingly, even though Mars has a very thin atmosphere, it fades away more slowly because of the planet's weaker gravity (it has a greater "scale height"). So the Karman line for Mars is thought to be about the same as for Earth, or three to four times the height of Olympus Mons. No orbiting satellite is going to collide with a Martian mountain.
You could certainly imagine a Martian atmosphere more tenuous than it actually is, so that the Karman line is only 20 km up, less than the 25 km height of Olympus Mons. In that sense, I agree with Brick that the answer can only be Yes. But the atmosphere in that case would be very thin indeed.
It would be interesting to know the thickest possible atmosphere for which a mountain can extend past the Karman line, but I don't have that answer.