Consecrated in February 1886 at St Paul's Cathedral by Archbishop Benson, as Missionary-Bishop of the Church of England in Japan, Bickersteth arrived at Nagasaki on 13 April the same year.

[9] In February 1887, at a meeting in Osaka instigated by Bickersteth and presided over by Bishop Channing Moore Williams, it was agreed to unite the various Anglican missionary efforts in Japan into one autonomous national church; the Nippon Sei Ko Kai.

[13] The travel journal of Mary Jane Bickersteth,[14] who accompanied the tour of Japan, includes detailed descriptions of the Anglican church's mission work, visits to sites such as the Shrines and Temples of Nikkō, a meeting with Fukuzawa Yukichi and the experience of surviving the strong Mino–Owari earthquake at Osaka on 28 October 1891.

[15] Bickersteth, suffering from failing health brought on by overwork, died on 5 August 1897 at Chiseldon, Wiltshire shortly after speaking on "The Development of Native Churches" at the opening meetings of the Fourth Lambeth Conference.

[16][17] Bickersteth's funeral and interment at Chiseldon was attended by, among others, Bishop John McKim of North Tokyo and Sir Ernest Satow, British Envoy to Japan.