While it is not uncommon for athletes to use foot orthoses to relieve pain and improve sports performance, little has been known about their effects on basketball performance. Free-throw basketball shooting is very important. However, fatigue deteriorates postural balance which might decrease free-throw shooting performance. This study investigated the effects of foot orthoses on dynamic balance and accuracy performance during free-throw shooting before and after physical fatigue was induced. Thirteen male recreational basketball players were tested with two foot orthoses (medial-arch support versus flat control) and fatigue conditions (before and after fatigue), when they performed standard free-throw shooting on a force platform. Results revealed that fatigue significantly increased coefficient of variance of medial-lateral center of pressure (CoP) excursion when participants worn flat control orthoses (p < 0.05). Meanwhile, foot orthoses improved dynamic balance during shooting as they significantly reduced total resultant and anterior-posterior sway excursions as well as resultant and anterior-posterior CoP velocities, and base of support area. Although this study found that fatigue and orthoses did not significantly affect the scores gained by free-throw shooting, the significant improvements in dynamic balance during shooting with the use of foot orthoses could have considerable impact on motor control during basketball shooting.