On June 1, 1939 he received news of his appointment as Vicar Apostolic of Masaka.
Archbishop Joseph Kiwanuka was the first native African Catholic to be ordained bishop in Sub-Saharan Africa.
In January 1961, Dr. Joseph Kiwanuka was appointed Archbishop of Rubaga, on the retirement of Archbishop Joseph Cabana. In October of the following year, he played a prominent role in the celebrations accompanying the attainment of political independence in Uganda.
On June 1, 1939 he received news of his appointment as Vicar Apostolic of Masaka. Joseph Kiwanuka was consecrated bishop in St. Peter's Basilica, Rome, by Pope Pius XII on October 29, 1939, assisted by Archbishop Henri Streicher.
In January 1961 Joseph Kiwanuka was appointed Archbishop of Rubaga and on 18 October, 1964. Bishop Kiwanuka assisted Pope Paul VI at the canonization of the twenty-two Catholic Martyrs of Uganda.