Monocarboxylate transporter 6 (MCT6; SLC16A5) is a recently studied drug transporter that currently has no annotated endogenous function. Currently, only a handful of compounds have been characterized as substrates for MCT6 (e.g., bumetanide, nateglinide, probenecid, and prostaglandin F2α (PGF2α)). The objective of our research was to characterize the MCT6-specific transporter kinetic parameters and MCT6-specific in vitro and in vivo interactions of PGF2α. Murine and human MCT6-mediated transport of PGF2α was assessed in MCT6-transfected oocytes. Additionally, endogenous PGF2α and a primary PGF2α metabolite (PGFM) were measured in plasma and urine in Mct6 knockout (Mct6−/−) and wild-type (Mct6+/+) mice. Results demonstrated that the affinity was approximately 40.1 and 246 µM respectively, for mouse and human, at pH 7.4. In vivo, plasma PGF2α concentrations in Mct6−/− mice were significantly decreased, compared to Mct6+/+ mice (3.3-fold). Mct6-/- mice demonstrated a significant increase in urinary PGF2α concentrations (1.7-fold). A similar trend was observed with plasma PGFM concentrations. However, overnight fasting resulted in significantly increased plasma PGF2α concentrations, suggesting a diet-dependent role of Mct6 regulation on the homeostasis of systemic PGF2α. Overall, these results are the first to suggest the potential regulatory role of MCT6 in PGF2α homeostasis, and potentially other PGs, in distribution and metabolism.