[1] According to accounts in the official court chronicle, Shahjahannama, the Jama Masjid originated from an imperial decree by Mughal emperor Shah Jahan in the year 1637.

Shah Jahan's eldest daughter, the princess Jahanara Begum, requested permission from the emperor to personally endow the new mosque, which was granted.

This was one of several reconstruction projects of the period in Mughal Agra, and represented a renewed attempt at building a congregational mosque for the city; the construction of one had commenced earlier by the Yamuna river, but this was interrupted and abandoned when attention was diverted towards completing the Taj Mahal.

The pishtaq features Persian inscriptions (largely praising the rule of Shah Jahan), executed as black letters inlaid in white marble, similar to the Taj Mahal.

[5] The prayer chamber is topped by three bulbous domes, which are decorated in a herringbone (zigzag) pattern of red and white stone.

[1][7] An engraving of this mosque from a painting by William Purser appears in Fisher's Drawing Room Scrap Book, 1832 together with a poetical illustration by Letitia Elizabeth Landon.