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Abstract Naturally occurring chlorate (ClO₃⁻) has been observed on Earth and potentially plays important roles in hydrology and mineralogy on Mars. However, natural sources of chlorate are uncertain. Here, we quantify the importance of atmospheric sources of chlorate. We use GEOS‐Chem, a global three‐dimensional chemical transport model, to simulate the formation, photochemical loss, transport, and deposition of atmospheric chlorate on present‐day Earth. We also develop a method to estimate the¹⁷O‐excess (∆¹⁷O) and the³⁶Cl‐to‐total‐Cl ratio (³⁶Cl/Cl) of atmospheric chlorate to interpret the observed isotopic composition of chlorate accumulated in desert soils. The model predicts that gas‐phase chemistry can produce 15 Gg Cl year⁻¹of chloric acid (HClO₃), which predominantly is taken up by aerosols to form particulate chlorate. Comparing the model with observations suggests that particulate chlorate undergoes chemical loss in the atmosphere, which controls the amount reaching Earth's surface. We show that the initial ∆¹⁷O that atmospheric chlorate acquires during formation would be erased rapidly in acidic aerosols due to the exchange of oxygen atoms with water. The analysis of³⁶Cl/Cl does not preclude a partial stratospheric origin for chlorate deposits in the Atacama Desert. In Death Valley, aqueous‐phase oxidation of oxychlorine species and anthropogenic activities potentially have greater influence. Our findings highlight the need for more observations of atmospheric chlorate and laboratory measurements of its reactivity in acidic conditions. Atmospheric chemistry should be considered in the future studies of the origin of chlorate on Mars.