Background Multiple intrinsic and extrinsic soft tissue structures that apply forces and support the medial longitudinal arch have been implicated in pes planus. These structures have common functions but their interaction in pes planus is not fully understood. The aim of this study was to compare the cross-sectional area (CSA) and thickness of the intrinsic and extrinsic foot muscles and plantar fascia thickness between normal and pes planus feet. Methods Forty-nine adults with a normal foot posture and 49 individuals with pes planus feet were recruited from a university population. Images of the flexor digitorum longus (FDL), flexor hallucis longus (FHL), peroneus longus and brevis (PER), flexor hallucis brevis (FHB), flexor digitorum brevis (FDB) and abductor hallucis (AbH) muscles and the plantar fascia were obtained using a Venue 40 ultrasound system with a 5–13 MHz transducer. Results The CSA and thickness of AbH, FHB and PER muscles were significantly smaller (AbH −12.8% and −6.8%, FHB −8.9% and −7.6%, PER −14.7% and −10%), whilst FDL (28.3% and 15.2%) and FHL (24% and 9.8%) were significantly larger in the pes planus group. The middle (−10.6%) and anterior (−21.7%) portions of the plantar fascia were thinner in pes planus group. Conclusion Greater CSA and thickness of the extrinsic muscles might reflect compensatory activity to support the MLA if the intrinsic foot muscle function has been compromised by altered foot structure. A thinner plantar fascia suggests reduced load bearing, and regional variations in structure and function in feet with pes planus.