Thomas Joseph Walsh Jr. was born in Parker's Landing, Pennsylvania, the eldest son of Thomas and Helen Walsh. After attending public and parochial schools, he studied at St. Bonaventure's College in Allegany, New York. He was ordained to the priesthood by Bishop James Edward Quigley on January 27, 1900. He then served as a curate at St. Joseph's Cathedral until the following June 25, when he became chancellor of the Diocese of Buffalo and private secretary to Bishop Quigley. In 1907 Bishop Charles H. Colton sent him to further his studies in Rome at the Pontifical Athenaeum S. Apollinare, from where he earned a doctorate in canon law and later a doctorate in theology. Upon his return to Buffalo, he resumed his duties as diocesan chancellor and secretary to the bishop. He was named rector of St. Joseph's Cathedral in 1915.
On May 10, 1918, Walsh was appointed Bishop of Trenton, New Jersey, by Pope Benedict XV. He received his episcopal consecration on the following July 25 from Archbishop Giovanni Bonzano, with Bishops Dennis Joseph Dougherty and John Joseph O'Connor serving as co-consecrators. Bishop Walsh was among those, who with Christian Brother Barnabas McDonald, FSC, encouraged the Knights of Columbus to consider working with youth. To this end, in August 1922, Walsh addressed the annual meeting of the Supreme Council of the Knights of Columbus held in Atlantic City. Supreme Knight James A. Flaherty named a special committee headed by then Deputy Supreme Knight, Martin H. Carmody to study the feasibility of organizing a junior order, which in 1925 became the Columbian Squires. Walsh was great advocate for Catholic education. In 1910, five sisters of the Religious Teachers Filippini were sent by Pope Pius X to work among the Italian immigrants in St. Joachim's parish in South Trenton. Walsh became a supporter of their work, and in 1918, with the help of a donation from businessman James Cox Brady, he acquired the Harvey Fisk estate "Riverside" in Ewing Township for the sisters. It became their motherhouse and novitiate. The sisters named it Villa Victoria in memory of Brady's wife, Victoria May Pery Brady. In 1933, the sisters established Villa Victoria Academy, an all-girls, private, Catholic middle and high school. He also dedicated the new St. James High School and Auditorium which later came to be known as Red Bank Catholic High School.
Following the death of Bishop O'Connor in May 1927, Walsh was named Bishop of Newark on March 2, 1928. He was installed at the, as yet unfinished, Cathedral of the Sacred Heart on the following May 1. The following year, Walsh established the Newark Mount Carmel Guild to help those on public assistance. In 1930, the guild set up a soup kitchen in the basement of St. Patrick's Pro-Cathedral. In 1930, Bishop Walsh acquired the "Tower Hill", the estate of Louis C. Gillespie, founder of L.C. Gillespie & Sons, importers of shellac. He invited the Religious Teachers Filippini to expand their work to the Diocese of Newark. The sisters re-located their motherhouse to Morristown and named it Villa Walsh, where they opened another girls school, Villa Walsh Academy, while continuing to operate Villa Victoria Academy in Ewing Township. In 1931, Bishop Walsh saw the opening of a new chancery building on Mulberry St. Prior to that the administration of the diocese was conducted out of offices at St. John's School. In 1933, Bishop Walsh established Saint Gertrude Cemetery in Colonia, New Jersey. In 1935, Walsh attended a Eucharistic congress held in Cleveland. He raised $2 million in 25 days to build Immaculate Conception Seminary in 1936, and encouraged Seton Hall Preparatory School and Seton Hall College to receive state accreditation. Walsh was a close friend of Abbot Patrick Mary O'Brien, of St. Mary's Abbey in Morristown. Upon the elevation of the Diocese of Newark to the rank of archdiocese by Pope Pius XI, Walsh was appointed its first Archbishop on December 10, 1937. He received the pallium on April 27, 1938. He convened a synod in 1941. In September 1947, Archbishop Walsh gave the opening convocation at the New Jersey Constitutional Convention. Archbishop Walsh passed away on June 6, 1952 and was buried in the Cathedral crypt where Bishop O'Connor had previously been laid to rest.