Fernando Ferrer, the MTA's current vice chairman, will become the acting chairman.
Mayor Bill de Blasio discussed Lhota on WNYC-AM radio and praised Ferrer, who the mayor noted he supported when he ran for mayor.
The mayor stressed that the MTA's bigger issue is funding from Albany.
"No one is going to be able to get the work done to fix the subways and buses if we don't have a permanent funding source," de Blasio said on the radio.
Governor Andrew Cuomo's administration and MTA will immediately begin a search for a new chairman. As Cuomo enters his third term, more departures are expected.
In a tweet, Cuomo praised Lhota's tenure.
Joe Lhota has dedicated decades of his life to public service culminating in two tours of duty at the helm of the MTA. He stabilized the subway system, appointed a new leadership structure, and led with a steady hand during some of the agency’s most challenging moments.— Andrew Cuomo (@NYGovCuomo) November 9, 2018
"Joe Lhota has dedicated decades of his life to public service culminating in two tours of duty at the helm of the MTA. He stabilized the subway system, appointed a new leadership structure, and led with a steady hand during some of the agency's most challenging moments. In short, Joe demonstrated time and again why he was the right person for the job. I am deeply grateful for his service to the State of New York," it read.
Lhota is a career public servant, moving between public and private jobs, which have raised questions of conflict of interest.
Lhota, however, never even took the $1 a year he was offered for the MTA job.
At the MTA's board meeting last month, Lhota was asked about whether he had considered resigning over his possible conflicts of interest.
"The premise is wrong. I did not consider resigning from the MTA ... I never did," he said.
When asked how much longer he would hold the position, Lhota answered, "My term ends on June 2021. That's my term."
It's not yet clear what led to the resignation.
* Follow us on YouTube
* More local news
* Send us a news tip
* Download the abc7NY app for breaking news alerts