Akbar's Church built in 1598 was the first Catholic Church of Agra and it was the Cathedral of Agra till 1848. The Church was built by the Jesuit Fathers under Akbar's order. It was a gift from the Mughal Emperor Akbar. In this Church the Mughal Emperors came to pray, especially Jahangir. Emperor Jahangir finding the Church built by his father, Akbar too small, donated a large sum of money for a larger and more beautiful Church to be built.

Two eminent Catholics, Khwaja Martins and Mirza Sikandar Junior contributed generously towards the extension of this Church.

In 1632 Emperor Shah Jahan declared war on the Portuguese. He defeated them in 1634. He brought over 4000 prisoners to Agra, all Christians. They underwent persecution and so did the Jesuit Fathers. In 1635 Shah Jahan released the Jesuit Fathers on condition that they pulled down their Church. This was done. However in 1636 the Emperor allowed the Fathers to rebuild the Church with the material of the ruined Church. On September 8,1636 the first Holy Mass was celebrated in this reconstructed Church. It underwent great changes during the course of the next two centuries.

In 1758 the Persian Invasion under Ahmed Shah Abdali shattered the Mughal supremacy. During the siege of Agra, the Church was ransacked by the Persian soldiers.

In 1769 Walter Reinhardt then Commander of Agra Fort helped Father Wendel S.J. to rebuild the Church and make an extension. In 1835 Bishop Pezzoni with the generous aid from Sir John Baptist Filose extended the Church westward.

This Church has witnessed many a historical event In 1610 to this Church came the three Royal Princes, nephews of the Emperor Jahangir to be baptized by Rev. Fr. Corsi, S.J. and Fr. Xavier S.J. In this Cathedral was baptized the Begum Johana Sumroo, the Begum of Sardhana. It was in this Cathedral the Religious of Jesus and Mary from France were welcomed by Bishop Borghi in 1842. It was the proud privilege of Bishop Borghi to consecrate in this historic Church Msgr. Carli Bishop of Almira in 1843 and the Servant of God Bishop Anastasius Hartmann, Vicar Apostolic of Patna in 1846.