Time of day can influence cocaine-seeking behavior in rats, and this influence may depend on the suprachiasmatic nucleus (SCN). We used western blots to measure expression of dopamine transporter (DAT) and tyrosine hydroxylase (TH) proteins in the medial prefrontal cortex (mPFC), nucleus accumbens (NAc), and caudate in sham and SCN-lesioned (SCNx) rats at ZT4 (Zeitgeber time 4, 4 h after lights-on) or ZT20 (8 h after lights-off). In the mPFC, DAT levels were lower at ZT20 than at ZT4 in sham but not SCNx rats. In the NAc, DAT expression was higher at ZT20 than at ZT4, and this effect was blunted in SCNx rats. Caudate DAT levels were unaffected by time of day or SCNx. Levels of TH did not change in mPFC with time of day or SCN lesion; TH levels were higher at ZT20 in the NAc, with a trend towards higher levels at this time in SCNx rats. Caudate TH expression was slightly elevated at ZT20 in sham but not in SCNx rats. We conclude that DAT and TH within these brain regions exhibit diurnal variation and dependence on the SCN. The results may have implications for new strategies to maximize pharmacological treatments for drug addiction.