Background: Functional flatfoot induces medial longitudinal arch collapse and neuromuscular imbalance between intrinsic and extrinsic foot muscles. While targeted foot core training is a standard intervention, the influence of weight-bearing postures on the selective activation of these muscles remains biomechanically ambiguous. Objects: This study aimed to investigate the electromyographic (EMG) activity of the abductor hallucis (AH) and tibialis anterior (TA) under different weight-bearing conditions and specific foot core exercises in individuals with functional flatfoot. Methods: Thirty young adults with functional flatfoot participated in this cross-sectional study. Surface EMG was utilized to measure the muscle activity of the AH and TA during three exercises: short foot (SF), toe curl (TC), and toe spread (TS). Each exercise was performed under two weight-bearing conditions: non-weight-bearing (sitting) and full-weight-bearing (standing). A 2 × 3 repeated measures ANOVA was conducted to analyze the main effects and interactions. Results: The interaction effect between posture and exercise type was not statistically significant for either the AH (p = 0.145) or TA (p = 0.661). Furthermore, weight-bearing posture yielded no significant main effect on muscle activation. However, the type of exercise demonstrated a highly significant main effect (p < 0.001). Post-hoc analysis revealed that AH activation was significantly greater during SF and TS compared to TC (p = 0.002), with no significant difference between SF and TS. Conversely, TA activation was significantly higher during TC than during SF and TS (p < 0.001). Conclusion: Weight-bearing posture does not dictate the magnitude of foot muscle activation; rather, specific exercise kinematics drive selective neuromuscular recruitment. Clinicians can safely prescribe the SF and TS exercises in a seated position to optimally isolate the AH without inducing compensatory TA hyperactivation, thereby providing a secure and targeted rehabilitation strategy for flexible flatfoot.