The isotopic signature of atmospheric carbon offers a unique tracer for the history of the Martian atmosphere and the origin of organic matter on Mars. The photolysis of CO2 is known to induce strong isotopic fractionation of the carbon between CO2 and CO. However, its effects on the carbon isotopic compositions in the Martian atmosphere remain uncertain. Here, we develop a 1D photochemical model to consider the isotopic fractionation via photolysis of CO2, to estimate the vertical profiles of the carbon isotopic compositions of CO and CO2 in the Martian atmosphere. We find that CO is depleted in 13C compared with CO2 at each altitude, due to the fractionation via CO2 photolysis: the minimum value of the δ
13C in CO is about −170‰ under the standard eddy diffusion setting. This result supports the hypothesis that fractionated atmospheric CO is responsible for the production of the 13C-depleted organic carbon in the Martian sediments detected by the Curiosity Rover, through the conversion of CO into organic materials and their deposition on the surface. The photolysis and transport-induced fractionation of CO that we report here leads to a ∼15% decrease in the amount of inferred atmospheric loss when combined with the present-day fractionation of the atmosphere and previous studies of carbon escape to space. The fractionated isotopic composition of CO in the Martian atmosphere may be observed by ExoMars Trace Gas Orbiter and ground-based telescopes, and the escaping ion species produced by the fractionated carbon-bearing species may be detected by the Martian Moons eXploration mission in the future.