The Most Rev Justin Welby visited St Sebastian's Church in the seaside town of Negombo just after arriving for a three-day visit to the country.
More than 100 people died in the attack on the church in Negombo, which is known as The Little Rome due to its dense Catholic population.
A total of 263 people were killed when seven suicide bombers from a local Muslim group attacked three churches and three luxury hotels on April 21, in the worst violence by the Islamic State group-linked militants in South Asia.
Quoting a sermon by Pope Francis's personal preacher delivered to the Queen years ago, Mr Welby said: "When they come to kill us do they ask if we are Christians or Pentecost or Presbyterian or Catholic? They ask only if we are Christian.
"So when on Easter morning I heard of the terrible events in this church and other places in Sri Lanka, we knew that our sisters and brothers have been killed and wounded and we kept silence and prayed for you."
Mr Welby was welcomed by the Archbishop of Colombo, Cardinal Malcolm Ranjith.
He knelt and bowed down on the glass-covered tiled floor where the suicide bomber set off the explosives at Easter Mass. The pockmarked area is preserved as a memorial.
Mr Welby is also expected to meet Sri Lanka's PM Ranil Wickremesinghe and preside over a service in an Anglican cathedral in Colombo.
Deeply moving to be at St Sebastian's Church in #Negombo this morning, with families of Christians killed in the #SriLanka terrorist attacks on Easter Sunday. You are not alone. The Christian community around the world will not forget you. We pray for you. Jesus remains with you. pic.twitter.com/qothGVJIlX
— Archbishop of Canterbury (@JustinWelby) August 29, 2019
His visit comes a month after Cardinal Ranjith - Sri Lanka's most senior Roman Catholic - called for an independent and transparent commission to investigate the Easter attacks, saying justice had not yet been served.
Sri Lankan leaders and the security establishment are under fire for not acting on near-specific intelligence on possible attacks on churches. Government leaders have acknowledged some intelligence units were aware of possible attacks weeks before the bombings.
President Maithripala Sirisena has said he had been kept in the dark on intelligence about the planned attacks and vowed to "take stern action" against officials who failed to share it. He later appointed a presidential commission to investigate.
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