Lynn supervised hundreds of priests in his role as secretary for clergy at the Archdiocese of Philadelphia.
Last month he became the most senior clergyman convicted in connection to the US Roman Catholic Church scandal.
Judge M Teresa Sarmina said Lynn enabled “monsters in clerical garb… to destroy the souls of children”.
The sentence handed down was less than the maximum seven-year penalty that prosecutors had sought for Lynn’s conviction on one count of child endangerment.
Lynn was found guilty of endangering the victim of Edward Avery, a former priest convicted in 1999 of sexual assault.
He had declared Avery guilty of an earlier complaint by 1994, and helped steer him into a treatment programme. But he also knew that Avery was later sent to live in a new parish, where he assaulted an altar boy.
Lynn was found not guilty of another charge of child endangerment and conspiracy.