Physical activity (PA) promotes brain health in a variety of domains including cognition, mood, and neuroplasticity. At the neurochemical level, the mechanisms underlying these effects in the brain are not fully understood. With proton Magnetic Resonance Spectroscopy (1H-MRS), it is possible to non-invasively quantify metabolite concentrations, enabling studies to obtain measures of exercise-induced neurochemical changes. This systematic review aimed to examine the existing literature on acute effects of PA on brain metabolites as measured by 1H-MRS. Four databases (Cochrane Central Register of Controlled Trials, PubMed, Embase, and PsycINFO) were searched, identifying 2965 studies, of which 9 met the inclusion criteria. Across studies, Gamma-AminoButyric Acid (GABA) and lactate tended to increase after exercise, while no significant changes in choline were reported. For glutamine/glutamate (Glx), studies were inconclusive. Conclusions were limited by the lack of consensus on 1H-MRS data processing and exercise protocols. To reduce inter-study differences, future studies are recommended to: (1) apply a standardized exercise index, (2) consider the onset time of MRS scans, and (3) follow standardized MRS quantification methods.