This study examines the agreement between photolysis frequency measurements by the NCAR scanning actinic flux spectroradiometer (SAFS) and calculations from a cloud-free model (CFM) and investigates the impact of these differences on ozone photochemistry. Overall, the mean jNO2measurement to model ratio for all flights of TRACE-P was 0.943 ± 0.271. The sky conditions during the Transport and Chemical Evolution over the Pacific (TRACE-P) experiment were determined to be “cloud-free” 40% of the time; hence a CFM is frequently not representative of the local atmospheric conditions. Our analysis indicates that clouds have a larger impact on photolysis frequencies (from −90 to +200%) than do aerosols (maximum of ±20%). The CFM and SAFS jNO2 and jO(1D) values differed by 9% and 0–7%, respectively, during a vertical profile through a cloud-free and low AOD atmosphere. This suggests that measurement/model agreement to less than 10% may be difficult without better aerosol optical parameter inputs even under low-AOD conditions. For the TRACE-P chemical environment, OH, NO, and HO2 were more sensitive than other compounds (e.g., CH3C(O)O2, CH3OOH) to changes (or errors) in photolysis frequency inputs to a photochemical box model. Compounds including NO2, PAN, and HCHO exhibited different relationships to j-value changes below and above the boundary layer. Ozone production and loss rates increased linearly with changes (or errors) in the photolysis frequency with the resulting net O3 tendency increasing with a linear slope near unity. During the TRACE-P mission the net photochemical effect of clouds and aerosols was a large decrease in photochemical O3 production in the boundary layer.