The aim of this study was to evaluate the performance of the Aqua–MODIS (MYD04) Collections 5.1 (C051) and 6 (C006) operational aerosol products over Pakistan. These include the Dark Target (DT) and the Deep Blue (DB) C051/C006 aerosol optical depth (AOD) observations at 10 km spatial resolution, and which were validated using seven years (2007–2013) AOD measurements from two AERONET stations located in Pakistan’s two largest cities, Lahore and Karachi. Lahore is an inland city, consisting of built–up areas and agricultural land and dominated by mainly fine aerosol particles. Karachi is an urban–coastal city with built–up areas and bare land, and mainly affected by coarse aerosol particles. The retrieval uncertainties and accuracy were evaluated using the expected error over land (EE: ± 0.05 + 15%), the root–mean–square error (RMSE), the mean absolute error (MAE), and the relative mean bias (RMB). It was found that the DT C051 AOD retrievals were significantly overestimated over both AERONET sites with mean overestimation of 21% and 31% for Lahore and Karachi respectively. On the other hand, the DB C051 retrievals were underestimated by 10% and 35% for both cities. Similar to the DT C051, the C006 AOD retrievals were overestimated over Lahore, but significantly improved over Karachi as the mean overestimation reduced from 31% (RMB = 1.31) to 4% (RMB = 1.04) and the percentage of retrievals within the EE increased from 38.46% to 63.33%. However, the DB C006 AOD retrievals have similar errors (RMSE and MAE) and the percentage of retrievals within the EE over both cities as C051, but they have more mean underestimations. Spatio–temporal distributions showed that the DT and DB C006 were well correlated with Karachi and Lahore AERONET measurements respectively. Therefore, these results recommend the use of the DT C006 algorithm over Karachi and the DB C006 over Lahore for qualitative regional air quality applications due to differences in land cover characteristics and aerosol types.