The Rev. David Ajemian leaves court after pleading guilty to disorderly conduct.
He said he never meant to cause anxiety or to upset anyone.
"I recognize that what I did was disorderly and I'm glad the people of New York have accepted that," Ajemian said as he left court. "I plan to return to the Archdiocese of Boston and I hope to return to ministry duties."
Judge Rita Mella ordered Ajemian to pay a $95 court charge and signed a two-year order of protection directing him to stay away from O'Brien.
The Roman Catholic priest was arrested while trying to enter the NBC building in Manhattan for a taping of "Late Night With Conan O'Brien" despite being warned to stay away by the network's security personnel.
On Friday, a judge found him fit to stand trial despite claims of psychiatric issues.
Ajemian, who allegedly began writing to O'Brien in September 2006, has been placed on leave by the Boston Archdiocese. He was removed in June from his last posting at St. Patrick Parish in Stoneham after two years.
Ajemian attended Harvard University at the same time as O'Brien, but it is unclear whether the two crossed paths there.