Byford shared the news during a Metropolitan Transportation Authority board meeting.
"I'm very proud of what we have achieved as a team over the past two years and I believe New York City Transit is well-placed to continue its forward progress now that the MTA has a record-breaking $51.5 billion Capital Program in place," he said in a statement. "I'm very grateful to Gov. Cuomo, Chairman Foye and members of the Board for giving me the opportunity to serve New York and to head up North America's largest transit system."
Byford will stay on the job until Feb. 21. It is unclear who is successor will be.
WEB EXTRA: Read Byford's resignation letter (pdf)
Byford has held the position for just over two years and previously had similar roles in Toronto, Sydney, and London. During his time with the MTA he has been praised for turning it around by upgrading equipment, cleaning up stations, improving "on time" service and increasing ridership, CBS2's Hazel Sanchez reported.
MTA Chairman & CEO Patrick Foye called it a "successful two years of service" and thanked him for his work.
"Andy was instrumental in moving the system forward, enacting the successful Subway Action Plan and securing record capital funding with the governor and the Legislature, and we wish him well in his next chapter," Foye's statement continued.
When asked why, specifically, Byford decided to resign, Foye said, "Andy's reasons were personal and I respect those."
Riders Alliance Executive Director John Raskin also praised Byford for his work on behalf of commuters.
"Subway and bus riders are grateful to Andy Byford for his historic service at New York City Transit. In two years, Andy made subways faster and more reliable, he tackled longstanding challenges to improving bus service, and he crafted the first plan in a generation that would truly modernize the transit system," Raskin said in a statement.
Mayor Bill de Blasio reacted to the news on Twitter, writing, "This is a real loss for New York City's subway and bus riders. The MTA needs people like Andy Byford -- now more than ever."
New York City Council Speaker Corey Johnson said in a tweet he was "devastated" by the news, later adding Byford's departure could slow down his Fast Forward Plan to transform and modernize subway and bus service.
"Given that he has had such success, to see him leave in this way, it's going to be hard to find another person as capable as Andy Byford," Johnson said.
Public Advocate Jumaane Williams called it a "serious step backward."
As he indicated in his resignation letter, Byford quit because he resented having his job scaled back as part of the MTA reorganization plan, but he also clashed repeatedly with the governor.
Byford threatened to step down back in October, but later said, "I'm here to stay."
The transit president was missing from a Queens bus redevelopment meeting Thursday night, following the announcement of his resignation.
"I'm concerned that he won't be here at this meeting to hear our concerns," Queens resident Beverly Jones told CBS2's Valerie Castro.
It's unclear how much of a role Byford will still play until his last day.
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