Cells possess homeostatic mechanisms to regulate functions under stressful conditions. Among these mechanisms is the hypoxia-inducible factor (HIF). We aimed to characterize the expression of the HIFα protein in the crayfish brain, a putative pacemaker in this species, to determine if it exhibits a rhythm. Crayfish Procambarus clarkii were acclimated to a 12:12 light–dark cycle (LD 12:12), while others were kept in constant darkness (DD) for an additional 72 hours, in both conditions, being killed at six time points. The brains were processed by western blot using a primary anti-HIF-1α antibody. Under LD, HIFα levels showed no significant daily variations. However, COSINOR analysis showed a bimodal rhythm. In the DD condition, significant differences were observed revealed a circadian rhythm. Our findings demonstrate that HIFα in the crayfish brain exhibits a circadian rhythm, suggesting its role as a master regulator in the circadian system feedback loop of the of these animals.