This shrine is located 12 km from Kampala Central along Jinja Road, Namugongo an established place of execution in traditional Buganda, is reminisced nowadays because of cold blood that was shed there on 3rd June 1886 at the order of KabakaMwanga.

In the last week of May, unknown number of Baganda men and men suspected or known to have been baptized were detained near Mengo and forced to march by some accounts naked while others were dragged on their back to the executing place - Namugongo, after which they were kept in captivity for a couple of days while a large pyre was being prepared.

While on the morning of 3rd June, those prisoners who had not already done so were given one final opportunity to renounce their recently assumed belief and no one of these coverts that accepted. Meanwhile one of the Martyrs by the names of Charles Lwanga who was the head of the catholic contingent was hacked apart and thrown into the fire there and then. On the following day, lasting converts were bound in reed mats and thrown on to the pyre and burnt alive.

Over 26 reminisced sufferers of the holocaust were all baptized and thus known to one; however contemporary reports indicate that more than 30 people were thrown into the fire. In a year 1920, Pope Benedict XV paved the way for future canonization by declaring blessed the 13 known catholic martyrs at Namugongo together with another nine catholic victims of separate killings in May 1886. The 22 catholic martyrs were finalized canonized during Vatican II conference by Pope Paul VI on 18 October 1964.

Pope Paul VI paid a visit to Uganda – the first reigning pope to set foot in Sub Saharan Africa to make pilgrimage at Namugongo in July 1969, where he instructed that a shrine and a church be built on the spot where Lwanga was executed. Namugongo Martyrs Church devoted in 1975 and subsequently named basilica church, is unusual and impressive building, metallic and modernistic in form however grounded on the traditional Kasiisira style.

The site was visited by Archbishop Robert Runcie of Canterbury in 1984 and in 1993 by Pope John Paul II. The execution of these converts on 3rd June still stands in the hearts of the people and is regarded as a public holiday in Uganda and is marked worldwide on the church calendar in honor of Uganda martyrs.