The customized insole is widely recommended as an effective intervention for pain reduction and foot function improvement in plantar fasciitis persons. However, it is unclear whether the additional correction of medial wedges could change the kinematics from the only insole. The objectives of this study were thus to compare customized insoles with and without medial wedges on lower extremity kinematics during gait and to determine the short-term effects of the customized insole with medial wedges on pain intensity, foot function, and ultrasonographic findings in plantar fasciitis persons. A within-subject, randomized, crossover design within motion analysis research laboratory was conducted among 35 persons with plantar fasciitis. Main outcome measures included joint motions of the lower extremity and multi-segment foot, pain intensity, foot function, and ultrasonographic findings. The customized insole with medial wedges produced less knee motion in the transverse plane and hallux motion in all planes during the propulsive phase than that without medial wedges (all p < 0.05). After the 3-month follow-up, the insoles with medial wedges decreased pain intensity and increased foot function. Abnormal ultrasonographic findings also decreased significantly after the 3-month treatment of insoles with medial wedges. Customized insoles with medial wedges seem superior to those without medial wedges on both multi-segment foot motion and knee motion during propulsion. Positive outcomes from this study supported the use of customized insoles with medial wedges as an effective conservative treatment in patients with plantar fasciitis.Trial registration: TCTR20210928006 (28/09/2021).