The Uganda Martyrs Shrine Parish Namugongo started as a sub-parish of Nsambya with a grass thatched church at Kyaliwajjala trading center, about a kilometer from the current location of the Shrine.
On 6th June 1920, as the Uganda Martyrs were being beautified in Rome, a young Dutch priest, Rev. Fr. Stephen Walters together with a group of pilgrims from Nsambya made a pilgrimage to the site where St. Charles Lwanga was martyred. It was during this pilgrimage that the priest conceived the idea of acquiring land and building of a church at this very spot.
This dream was realized when eight acres of land were bought around the spot of martyrdom of St. Charles, and this led to the transfer of the church from Kyaliwajja to Namugongo, construction of a small rectangular but beautiful structure and finally the appointment of Rev. Fr. Peter van Rooyen as the first parish priest of Namugongo Shrine Parish in 1935.
In 1967, His Eminence Emmanuel Cardinal Nsubuga decided to build a befitting Martyrs monument at the site; the current Martyrs Shrine.