Transport in the tropical lower stratosphere plays a major role in determining the composition of the entire stratosphere. Previous studies that quantified the relative role of transport processes have generally assumed well‐mixed tropics and focused on tropical‐wide average characteristics. However, it has recently been shown that there is a hemispheric difference in the annual cycle of tropical lower stratosphere ozone and other tracers, with a larger amplitude in the northern tropics (NT) than in the southern tropics (ST). In this study, we examined the ability of chemistry climate models (CCMs) to reproduce the hemispheric differences in ozone (O3) and other tracers (i.e., hydrochloric acid, or HCl and nitrous oxide, or N2O), and then use the CCMs to examine the cause of these differences. Examination of CCM simulations from the CCMVal‐2 project shows that the majority of the CCMs produce the observed feature of a larger annual cycle in the NT than ST O3 and other tracers. However, only around a third of the models produce an ozone annual cycle similar to that observed. Transformed Eulerian Mean analysis of two of the CCMs shows that seasonality in vertical advection drives the seasonality in ST O3 and N2O while seasonality of horizontal mixing drives the seasonality in NT O3 and N2O, with a large increase in horizontal mixing during northern summer (associated with the Asian monsoon). Thus, latitudinal and longitudinal variations within the tropics have to be considered to fully understand the balance between transport processes in tropical lower stratosphere.