The mosque of Isa Khan is located west of the mausoleum, which along with other buildings form the UNESCO World Heritage Site of Humayun's tomb complex.

It is situated south of the Bu Halima's garden in the Humayun's Tomb complex.

[3] Comprehensive restoration work was done through the Aga Khan Trust for Culture (AKTC), in collaboration with Archaeological Survey of India (ASI) in 2011-2015.

[5] The mausoleum is built mainly with grey quartzite with red sandstone used for ornamentation.

The square head doorway of the gate chamber has been built in Hindu architectural style.

The cenotaph of Isa Khan Niazi is made of red sandstone and marble.

[5] The mosque's central bay is made of red sandstone, the side-bays of grey stone.

[3] Each bay houses a four-arched gateway to the mosque, whose borders are decorated with green and blue tiles.

The medallions on the spandrels of these arches contain floral designs inlaid with blue and green tiles, a feature of Moorish architecture.