The moderating effect of early experience on gene-behavior associations has been well characterized. The molecular events that allow for such moderation are not well understood, however. We assessed the impact of early experience and serotonin transporter linked promoter polymorphism (rh5-HTTLPR) genotype on peripheral serotonin transporter (5-HTT) regulation in response to a maternal/social separation and relocation stressor in infant rhesus macaques. We further tested the hypothesis that modulation of 5-HTT regulation by rearing and/or genotype is mediated by glucocorticoid (GC) availability. Fifty-three infant (3–4 months of age) rhesus macaques that were either nursery reared (NR) or mother reared (MR) were genotyped for rh5-HTTLPR. Infants were blood sampled within 2.5 h of maternal or social separation/relocation and again 5 h later. Infants were then administered dexamethasone, a synthetic GC and blood sampled 16.5 h later. 5-HTT RNA was quantified from peripheral blood mononuclear cells. Plasma cortisol was measured at all time points. The MR individuals upregulated 5-HTT significantly during maternal/social separation, while NR individuals did not. Concomitant increases in cortisol were not observed, but dexamethasone treatment stimulated 5-HTT expression regardless of genotype/rearing group, and 5-HTT expression in the post-stressor sample was correlated with plasma cortisol levels at all time points. Our data indicate that early experience exerted a strong influence on 5-HTT regulation during a stressor in infant rhesus macaques independent of rh5-HTTLPR genotype. We also showed that GCs may stimulate 5-HTT expression but that there likely exist faster-acting transcriptional regulators of 5-HTT that are in place as a function of experience.