Levels of ozone depleting substances (ODSs) in our atmosphere are determined by production, emission, and loss processes. However, atmospheric models are forced by the specified mixing ratios of these ODSs rather than the more fundamental emissions-based forcing. To more accurately represent the physics and chemistry of climate change on atmospheric circulation and ODSs, and therefore future ozone recovery, it is desirable to switch from the current highly constrained mixing-ratio-based forcing to emissions-based forcing in general circulation models (GCMs). As a first step of this model transition, we have conducted a 45-year (1960–2005) emissions-based simulation of the three primary chlorofluorocarbons (CFC-11, -12, -113) using the GEOS coupled chemistry-climate model (CCM). The simulated CFC concentrations and their seasonal cycles are compared with AGAGE and NOAA-GMD observations to evaluate emissions and atmospheric transport. The simulated CFC-12 agrees well with the observations, indicating a good estimate of emission and atmospheric loss. The simulated CFC-11 and CFC-113 shows high biases due to overestimate of emissions. Using tagged CFC tracers to track recent surface emissions and aged air masses transported downward from the stratosphere separately, we quantify the relative contribution of stratosphere-troposphere exchange (STE) and tropospheric transport to the seasonal cycles of CFCs in the lower troposphere. The seasonal cycles of CFCs in the lower troposphere are dominated by tropospheric transport of recent emissions during 1985–1994. The 1995–1999 period marks the transition period when variations due to fresh emissions and STE become equally important. Seasonal cycles of CFCs at most surface sites in the 2000–2004 period are dominated by STE. Seasonal cycles of CFCs due to STE show a late winter/early spring maximum and a summer/fall minimum. Seasonality of the tropospheric transport component at individual stations is governed by seasonal transport variations of fresh emissions from the polluted regions.