In this study, density functional theory (DFT) combined with time-dependent (TD) DFT calculations were employed to investigate the photoisomerization reaction kinetics of two near infrared (NIR) heptamethine cyanine (Cy7-NH3 and Cy7-SO3) dyes in the ground singlet state and the first excited singlet state. We found that the photoisomerization of the ground state all-trans Cy7 molecules results in at least one mono-cis and one all-cis species that demonstrate redshifted emission, in agreement with recently published transient state excitation modulation spectroscopy and fluorescence correlation spectroscopy measurements. The transition states were estimated for a whole photoisomerization pathway for both the ground singlet and first excited singlet state potential energy surfaces. We have found that all-cis isomers of the studied Cy7 dyes can be achieved through a sequential two-step photoisomerization within the excited singlet state potential energy surface, along the double CC bond adjacent to edge group (leading to mono-cis isomer 1) and along the double CC bond adjacent to the central-chain group (leading to mono-cis isomer 2). Computations show that all-trans→ mono-cis isomer 1→all-cis kinetics is limited by the first trans→ mono-cis isomer 1 stage, while the all-trans→ mono-cis isomer 2→all-cis pathway is limited by the second mono-cis isomer 2→all-cis stage. Accounting for the fact that mono-cis isomer 2 demonstrates red-shifted emission compared to the all-trans form and that this mono-cis isomer 2 is reachable through the energetically favorable all-trans→ mono-cis isomer 2 stage, we concluded that the experimentally observed red-shifted emission by Cy7-NH3 and Cy7-SO3 should be assigned to the formation of mono-cis isomer 2 species. If the all-cis isomer is populated through the double-step photoisomerization it can also be considered as a source of red-shifted emission. However, as follows from our simulations, the all-cis isomer is kinetically intricate to achieve compared to the mono-cis isomer 2.