He was CEO of X.com for less than a year and was fired by the board. Then they merged with the predecessor to PayPal, which was more successful. He become CEO of the merged company, but was again fired for poor technical decision making (among other things, he insisted that the company build on the Windows stack instead of Linux) before the company rebranded itself as PayPal.

So, technically he was never the CEO of "PayPal", just the company that became PayPal, and he got himself fired by the boards of both the companies that turned into PayPal. He retained 11% ownership of PayPal and ended up making a decent amount of money from the EBay acquisition.