Aerobic exercise may represent a useful intervention for drug abuse in predisposed individuals. Exercise increases plasticity in the brain that could be used to reverse learned drug associations. Previous studies have reported that exposing mice to a complex environment including running wheels after drug conditioning abolishes conditioned place preference (CPP) for cocaine, whereas running can enhance CPP when administered before conditioning. The purpose of the present study was to test the hypothesis that timing of exercise relative to conditioning has opposing effects on cocaine CPP. Male C57BL/6J mice experienced 30 days of running or sedentary treatments either before or after cocaine conditioning. Control animals always received saline and never cocaine, but otherwise underwent the same conditioning and exercise treatments. Animals were given bromodeoxyuridine injections at the onset of conditioning or exercise, and euthanized at the end of the study to quantify survival of new neurons in the hippocampus as a marker of plasticity. Wheel running accelerated extinction of CPP when running occurred entirely after drug conditioning, whereas running delayed extinction when administered before conditioning. A single conditioning day after running was sufficient to abolish the accelerated extinction observed when all conditioning preceded running. Running approximately doubled adult hippocampal neurogenesis, whereas cocaine had no effect. These results suggest that exercise-induced plasticity can facilitate learning that context is no longer associated with drug. However, if drug exposure occurs after exercise, running-induced plasticity may strengthen drug associations. The results provide insights into the interaction between exercise and drug conditioning that could have implications for drug abuse treatments.