Neuromuscular activation during and chronic adaptation from exercise are innately linked and both can vary along a muscle's length. During high-force and high-speed exercise, intramuscular hypertrophy follows set patterns that provide the greatest biomechanical advantages. However, it is unknown if muscle activity as recorded by surface electromyography (sEMG) will follow these patterns. The purpose of the present study was to compare vastus lateralis intramuscular sEMG during the heavy squat (HS) and unloaded jump squat (JS) exercises. Ten subjects performed HS with 80% of maximum load and unloaded JS to parallel-depth, while intramuscular peak sEMG and mean sEMG were measured at 33% (proximal), 50% (middle), and 67% (distal) thigh length. Muscle activity was compared between regions and exercises using a 3 × 2 repeated measures ANOVA with Bonferoni post hoc corrections. Peak sEMG was greater proximally in JS than HS (p = 0.033), but similar in the middle and distal regions (p = 0.521, 0.594, respectively), whereas mean sEMG was similar between all regions (p = 0.150–0.979). In addition, a main effect was found in which peak and mean sEMG were greater proximally than the middle and distal regions (p = 0.001, 0.006). Muscle activity measured using sEMG displayed dissimilar patterns to previously observed regional hypertrophy. Specifically, although previous research found greater proximal hypertrophy in JS than HS, in the present study peak sEMG was greater in HS than JS. Furthermore, distally where HS elicited greater hypertrophy than JS, no differences in sEMG were present. Thus, regional sEMG appears not to be a viable tool for predicting differences in regional hypertrophy, most likely due to technological constraints and intramuscular differences in muscle structure.