Saenz left with a gold parachute valued at $114.6 million, which comes on top of his $10.7 million salary from 2012.
Saenz, 70, was convicted in 2009 for making false accusations in a case concerning Banesto, a rival bank Santander acquired in 1994.
It was that merger that brought Saenz to Santander.
But the conviction includes an unusual twist. The government pardoned him in 2011, which meant he could keep his job. But this year, Spain's Supreme Court partly overturned that conviction, saying the government overstepped when it issued the pardon.
His criminal conviction was reinstated in February, which makes his ability to keep a job in the banking industry questionable, The New York Times reported.
Saenz is leaving before the issue comes to a head once again.
The bank said it was appointing a relatively unknown executive, Javier Marin, 47, to replace him.
Marin is currently the head of Santander's asset management, private banking and insurance operations, the Times said.