Activation changes in the prefrontal cortex (PFC) regions have been linked to acute exercise-induced improvements in cognitive performance. The type of exercise performed may influence PFC activation, and further impact cognitive function. The present study aimed to compare PFC activation during cognitive testing after moderate-intensity, high intensity, and yoga exercises, and to determine if PFC activation is linked to cognitive performance. Eight subjects (four male and four female), aged 35 ± 5 completed a control, high intensity, moderate intensity, and yoga exercises followed by administration of a cognitive task (NIH Toolbox Fluid Cognition). Left and right PFC activation (LPFC and RPFC, respectively) were evaluated by measuring hemoglobin difference (Hbdiff) changes during post-exercise cognitive assessment using functional near infrared spectroscopy (fNIRS). Activation during the cognitive test was higher in the LPFC after moderate intensity exercise compared to control, high intensity, and yoga (5.30 ± 6.65 vs. 2.26 ± 2.40, 2.50 ± 1.48, 2.41 ± 2.36 µM, p < 0.05, respectively). A negative relationship was detected between LPFC and processing speed after exercise. PFC activation did not align with cognitive performance. However, acute exercise, regardless of type, appeared to alter neural processing. Specifically, less PFC activation was required for a given neural output after exercise.