Jenik was suspended in 2018 pending a Church investigation into the alleged assault, which reportedly took place in the 1980s while the American was pastor of a Bronx parish.
"Although the alleged incidents occurred decades ago, the Lay Review Board has concluded that the evidence is sufficient to find the allegation credible and substantiated," US Cardinal Timothy Dolan said at the time of the suspension.
The Vatican said Francis had accepted the 75-year old's resignation, without providing any further details on the case.
Jenik has denied repeatedly molesting Michael Meenan between the ages of 13 and 17 during trips to his country house.