According to archaeologists, on 24 May 1693 AD, 1104 AH, Emperor Aurangzeb ordered the construction of a mosque at Subedar Parbaz Khan for the Muslim soldiers guarding the area to offer five daily prayers. After receiving this instruction, he built a single-domed mosque in this area. The village where his soldiers stayed was named after Karan as Prabajpur village. Later after the construction of the mosque, the mosque was named Prabaj Shahi Mosque after his name. Apart from this, experts have drawn conclusions from the architectural features of the mosque such as Kudi Masjid (Khulna), Masjid Badi and coins from the Bagher Hat region, as well as other evidences, especially the Bagher Hat inscription of 863 AD (1459) and the Masjid Badti Masjid inscription of 870 AD (1165) during the reign of Sultan Barbag Sahib. That is, Masjid Bagher Hat, Prabajpur village of Kaliganj Upazila, and the eastern part of Hooghly River in India, which is now Ichamati, was under Muslim rule in the middle of that century, if not earlier than the fifteenth century. From the opinion of experts and the fact that the village and the mosque were named after Subedar Prabaj Khan, it is accepted that Prabajpur Shahi Mosque was built by Subedar Prabaj Khan. Later, when the mosque was brought to the attention of the Department of Archaeology, this department was involved in the renovation of the historic mosque.
The external rectangular dimensions of the mosque are 46 feet 9 inches by 33 feet 9 inches. The mosque has a square prayer hall measuring 21 feet 6 inches by 21 feet 6 inches. There was a spacious balcony measuring 6 feet 9 inches. But the present balcony is no more. According to archaeologists, Prabajpur Shahi Masjid is a domed mosque similar to Atiya Jame Masjid in Tangail, Shahi Masjid in Narayanganj and West Latron and Chamkati Masjid.

On the other hand, there were three domes on the balcony. Bengali 1362 AD When the mosque was renovated, a rectangular open courtyard with main balcony area was built along a small wall towards the main eastern wall of the mosque for Friday Jumma prayers. The main room of the mosque had a total of 4 doors on the balcony and on the south wall and one on each side of the balcony. There were also 6 doors in each of the front walls and the walls between the verandah and the main room, 6 for a total of 10 doors. The lower portion of the 4 doorways on the north and south sides has recently been partially closed by small thin walls. The main door of the mosque is 4.7 inches wide. The western wall of the mosque has 3 decorative arches. The mihrab of the middle khan is slightly flared and larger in size than the two flanking ones as per the custom. Its decorations are beautiful.
All three arches rest on multi-foliated and multi-sided pillars. Besides, there is a large design in the shape of a flag at the junction of the lines on the outer edge of the mehrab. And the spandrels have two lotuses in bloom. All three of the arches have designs of upright and perpendicularly curved bushes at the ends of the arch structure. There are three different designs. The one on the north side has large lotuses and designs blooming according to Palana. The central one has large flag designs on either side within the folds of curvature. And the one on the southern side shows a gathering of beautiful large lotuses in bloom. According to a source, 50 acres of land was donated for the maintenance of the mosque. But the present mosque occupies only 3 acres of land. Conservation is currently required under government management. Accommodation for tourists has become essential.