The disturbed accused arsonist charged in a subway fire that killed an MTA conductor was ordered held without bail Saturday.

A day after his arrest in the case, Nathaniel Avinger, 50, was arraigned on a second-degree murder charge during a virtual court appearance in Manhattan Criminal Court.

Prosecutors said he started the March 27 fire on a Harlem No. 2 train that killed conductor Garrett Goble and injured 16 others.

“The fire completely destroyed the train car,” Assistant District Attorney Christine Keenan told a judge Saturday.

“The defendant admitted to being on the train lighting papers on fire, but claims he didn’t set the big fire.”

Prosecutors pointed to Avinger’s criminal history, alleging that two weeks before the subway incident he set a pile of garbage on fire at 125th Street in Harlem, causing a large blaze that damaged wiring on a lighting pole.

Avinger’s Legal Aid lawyer Marnie Zien asked that Avinger be offered some bail, but Judge Douglas Hoffman deemed him a flight risk and ordered him held.

Avenger has also been charged with third-degree sexual abuse for groping a female MTA employee.

His rap sheet also includes 13 misdemeanors, plus felonies including robbery and attempted assault.