Fitzpatrick succeeded Fenwick as the third Bishop of Boston upon the latter's death on August 11, 1846. The native Bostonian was warmly received his parishioners, and became popularly known as "Bishop John." His visitations in 1847 extended over nearly all his diocese, which then included the states of Massachusetts, Vermont, New Hampshire, and Maine. Following the outbreak of the Great Irish Famine, Fitzpatrick strongly encouraged Catholics to contribute to the relief effort in Ireland, declaring, "Apathy and indifference, on an occasion like this, are inseparable from crime!"; he later sent $20,000 to Archbishop William Crolly.