Ordained priest in 1884, he was a curate at Monkwearmouth before becoming Vice-Principal of the Clergy Training School in Cambridge. From 1892, he was Dean of Corpus Christi College, Cambridge before elevation to the colonial episcopate with his election as Bishop of Adelaide in March 1895. He was consecrated a bishop in Westminster Abbey and 23 May and was enthroned at Street Peter"s Cathedral, Adelaide on 4 July 1895.
In 1905, he was translated back to England when he was elected Bishop of Rochester.
He was enthroned at Rochester Cathedral in July 1905 and served for a quarter of a century before his retirement in 1930. Harmer died at Marine Cottage, Instow, and was buried at Rochester Cathedral.
His portraits remain at his former official residences of Bishop"s Court, Adelaide and Bishopscourt, Rochester.