Lynn, 61, had faced a maximum sentence of seven years in prison for his felony child endangerment conviction. He was cleared of three related charges at trial.
Lynn, the former secretary for clergy at the Archdiocese of Philadelphia, handled priest assignments and child sexual assault complaints from 1992 to 2004.
Judge M. Teresa Sarmina said that Lynn enabled "monsters in clerical garb ... to destroy the souls of children, to whom you turned a hard heart."
She added: "You knew full well what was right, Monsignor Lynn, but you chose wrong."
Lynn has been in prison since the June 22 jury verdict, when the trial judge revoked his bail.
Prosecutors had argued for the maximum sentence.
"His active, even eager execution of archdiocese policies - carried out in the face of victims' vivid suffering, and employing constant deceit - required a more amoral character, a striving to please his bosses no matter how sinister the business," prosecutors wrote in a sentencing memo filed Friday. "At any time during those 12 years, he could have had a moment of conscience."
The defense asked for a sentence of time served, probation or house arrest.
"The seven-year maximum sentence that the commonwealth advocates would serve no purpose at all - (it) would merely be cruel and unusual," Lynn's lawyers wrote in their sentencing memo.