Lynch studied at the diocesan Seminary of St. John the Baptist, then entered the Pontifical Urban College in Rome, where he graduated with a Doctor of Divinity degree.

[2] Lynch was ordained to the priesthood in Rome for the Diocese of Charleston on April 5, 1840 by Cardinal Giacomo Filippo Fransoni.

In the first year of the American Civil War, a major fire in December 1861 destroyed the cathedral, the bishop's residence and the diocesan library.

[2] On February 20, 1864, Lynch was named by President Jefferson Davis of the Confederate States of America (CSA) as its delegate to the Vatican.

Since the Vatican had never recognized the CSA, Lynch did not present his diplomatic credentials to Pius IX, who received him only in as a bishop.

During Lynch's audience, Pius suggested that "something might be done looking to an improvement in [the slaves'] position or state, and to a gradual preparation for their freedom at a future opportune time.

After the end of the war, US President Andrew Johnson pardoned Lynch for his role as Vatican delegate for the Confederacy.