A graduate of both Edinburgh and Cambridge Universities, he was ordained priest for the archdiocese of St. Andrews and Edinburgh, 15th June 1946, and subsequently continued his studies in Rome.

During his episcopate twelve new parishes were established, twenty-five churches built, of which seven were in existing parishes, and three Mass centres opened. Eight religious orders were introduced to the diocese. Diocesan structures were strengthened through the formation of a Pastoral Commission, Lay Council, Marriage Advisory Council, and Common Good Fund. Bishop Thompson took part in the last session of the Second Vatican Council in 1965. represented the Hierarchy at the first Synod of Bishops in Rome in 1967, and was first chairman of the Catholic Press Office in 1968.

He visited foreign missions in West Africa and South America in 1972. He was appointed by the Hierarchy in 1980 to plan the papal visit to Scotland in June 1982. On the grounds that at the age of 64 he did not have the “same energy, initiative, and capacity for active leadership as in earlier years” Bishop Thompson offered his resignation in September 1981 but this was not accepted until 14th December 1982 when he was appointed apostolic administrator of the diocese. On the translation of Bishop Devine, 13th May 1983, Bishop Thompson moved to Biggar as a parish priest. He died in Glasgow, 6th December 1987, and is buried in the precincts of his Cathedral.