In 1868, two new dioceses were created in Pennsylvania: Harrisburg and Scranton. Father Shanahan was named Harrisburg’s first Bishop. He was only 34 years old. He inherited a diocese the size of Belgium with 25,000 Catholics in a non-Catholic population of 500,000. One historian writes that “Central Pennsylvania has never been an easy soil for the seed of Catholicism to penetrate… but wherever Bishop Jeremiah Shanahan appeared bigotry disappeared, so great was the charm of his gentle, scholarly personality.”
Under Bishop Shanahan, the number of parishes rose from forty to 75, the number of priests increased from 22 to 51, and 22 parochial schools were founded. He introduced several religious communities to Harrisburg, the Sisters of Mercy and the Sisters of Charity. The years took a toll on his health, however, and he died of pneumonia at age 52 in September 1886. He was remembered as a
learned divine and scholar. He was noted for his charity, being among the very first always to reach the sick bed of the afflicted and dying. He was an uncompromising defender of his Faith and Church, and yet he understood the position of dissenting religionists, exercised justice and charity towards them, was free from bigotry, charitable to all, and won the confidence of the whole community, without distinction of creed. He possessed a ready and agreeable manner of imparting information to others, and, though he courted retirement, he was a genial companion, a charming conversationalist, and a true friend. He was thoroughly manly, kind hearted, gentle yet firm, and was large and broad in character, mind, and heart. He was conscientious as a Christian and as a citizen, and true as a friend.
In 1899, his brother John succeeded him as Harrisburg’s third Bishop.