The present study was undertaken to evaluate the performance of different algorithms for flattening filter-free (FFF) and flattened (FF) photon beams in three different in-homogeneities. Computed tomography (CT) image sets of the CIRS phantom maintained in the SAD setup by placing the ionization chamber in the lung, bone, and tissue regions, respectively, were acquired. The treatment planning system (TPS) calculated and the ionization chamber measured the doses at the center of the chamber (in the three mediums) were recorded for the flattened and non-flattened photon beams. The results were reported for photon energies of 6 MV, 10 MV, 15 MV, 6 FFF, and 10 FFF of field sizes 5 × 5 cm2, 10 × 10 cm2, and 15 × 15 cm2. In the bone inhomogeneity, the pencil beam algorithm predicted that the maximum dose variation was 4.88% of measured chamber dose in 10-MV photon energy for the field size 10 × 10 cm2. In water inhomogeneity, both the collapsed cone and Monte Carlo algorithm predicted that the maximum dose variation was ± 3% of measured chamber dose in 10-MV photon energy for the field size 10 × 10 cm2 and in 10-MV FFF photon energy for the field size 5 × 5 cm2, whereas in lung inhomogeneity, the pencil beam algorithm predicted that the highest dose variation was - 6.9% of measured chamber dose in 10-MV FFF photon energy for the field size 5 × 5 cm2. FF and FFF beams performed differently in lung, water, and bone mediums. The assessment of algorithms was conducted using the anthropomorphic phantom; therefore, these findings may help in the selection of appropriate algorithms for particular clinical settings in radiation delivery.