Justin Welby said he was praying "for Jesus Christ to comfort all those whose lives were changed forever by these evil acts".
Around 100 Christians died after a twin suicide bomb attack at All Saints Church in Peshawar, Pakistan, on 22nd September 2013.
Two bombs were detonated as almost 600 worshippers left the service near Qissa Khawani Bazaar, making it the worst attack on a church in Pakistan's history.
The explosives were laden with deadly ball bearings, designed to kill and maim as many as possible.
The archbishop said: "Firstly, our thoughts and prayers are with all those who were bereaved and injured in these terrible attacks.
"In May I visited Pakistan's Anglican community – who number 800,000 in a population of 180 million – and I was appalled to hear and see evidence of the hatred, violence and persecution they face.
"As I sat among them, I heard the searing anguish in their cry for the right to worship in freedom and safety. But I was also moved and inspired by their steadfastness and courage, which is grounded in deep and unshakable faith in Jesus Christ.
"In the days following the bombings, Christians in Peshawar spoke of forgiveness for their attackers even as they cried out for justice and protection.
"With one year passed, we should reflect again in awe on this profound witness to Christ by our brothers and sisters in their darkest moment of suffering.
"As we reflect on the Peshawar martyrs and their families and all those injured in those shocking attacks, we do so knowing with deep concern that the often deadly persecution of Christians and other minorities has further escalated in many places, especially Iraq and Syria.
"We look back knowing that our prayers are needed with fresh urgency, as we cry them out to a God who shares deeply in the pain, anxiety, suffering and despair of all those persecuted for their beliefs."
The anniversary of the attack has seen calls for the Pakistani government to do more to protect Christians in the country.
Anti-persecution charity Christian Solidarity Worldwide is urging authorities to pay the compensation that was promised.
Many of those injured had to leave hospital early because they could not afford to pay for treatment.
CSW's chief executive Mervyn Thomas said: "CSW stands in solidarity with the victims of this horrendous crime and calls for justice to be served and compensation to be delivered without further delay.
"We urge the government of Pakistan to be proactive in combating the threat of extremism, and to enact the ruling of the Supreme Court [to pay compensation] in order to ensure protection for places of worship and communities of minority faiths."