Padres general manager A.J. Preller added that the club will start its search for a new manager immediately.
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Murphy finished 2015 with a 42-54 record, after the firing of longtime manager Bud Black in June.
“I’m a little bit regretful I didn’t reveal myself earlier,” Murphy said, via The San Diego Tribune . “I felt I needed to stand back, earn some respect and earn some trust. It’s hard (to take over) on the run, but I learned a lot.
“All things being equal, I’d like another opportunity, an opportunity to really manage a team from spring training on. But there’s no guarantees. That’s not how life works.”