Physical activity (PA) is a non‐invasive, cost‐effective means of reducing chronic disease. Most US citizens fail to meet PA guidelines, and individuals experiencing chronic stress are less likely to be physically active. To better understand the barriers to maintaining active lifestyles, we sought to determine the extent to which short‐ versus long‐term PA increases stress‐ and aversion‐related markers in wild‐type (WT) and low voluntary running (LVR) rats, a unique genetic model of low physical activity motivation. Here, we tested the effects of 1‐ and 4‐weeks of voluntary wheel‐running on physiological, behavioral, and molecular measures of stress and Hypothalamic Pituitary Adrenal (HPA)‐axis responsiveness (corticosterone levels, adrenal wet weights, and fecal boli counts). We further determined measures of aversion‐related signaling (kappa opioid receptor, dynorphin, and corticotropin releasing hormone mRNA expression) in the basolateral amygdala (BLA), brain region well characterized for its role in anxiety and aversion. Compared to sedentary values, 1‐, but not 4‐weeks of voluntary wheel‐running increased adrenal wet weights and plasma corticosterone levels, suggesting that HPA responsiveness normalizes following long‐term PA. BLA mRNA expression of Prodynorphin (Pdyn) was significantly elevated in WT and LVR rats following 1‐wk of wheel‐running compared to sedentary levels, suggesting that aversion‐related signaling is elevated following short‐, but not long‐term wheel‐running. In all, it appears that the stress effects of acute PA may increase molecular markers associated with aversion in the BLA, and that LVR rats may be more sensitive to these effects, providing a potential neural mechanism for their low PA motivation.