Objective: To determine the effects of ultrasound therapy and neuromuscular electrical stimulation (NMES) application on the muscle architecture and functional capacity in patients with knee osteoarthritis. Design: A randomized study. Subjects: A total of 60 patients with knee osteoarthritis. Interventions: Participants were randomized into one of the following two intervention groups, five days a week, for three weeks: the combination of NMES application, hot pack, and exercise therapy was applied to the NMES group. The combination of therapeutic ultrasound, hot pack and exercise therapy was applied to the ultrasound therapy group. Main measures: Subjects were evaluated for pain and functional capacity with the use of the visual analog pain scale (VAS), Western Ontario and McMaster Universities Arthritis Index (WOMAC), and 15 meter walking test. The muscle architecture (muscle thickness, pennation angle and fascicle length) was assessed from vastus lateralis and quadriceps femoris muscles bilaterally by ultrasonography. Results: Two groups presented significant improvements in all outcome measures before and after treatment (P < 0.01). There were significant improvements in VAS rest pain (P < 0.05), VAS activity pain (P < 0.05), WOMAC pain (P < 0.05), WOMAC stiffness score (P < 0.05), and WOMAC physical function (P < 0.05) for the ultrasound therapy group in comparison to the NMES group. NMES group exhibited more increases in the muscle thickness and fascicle length values when compared to ultrasound therapy group (P < 0.05). Conclusion: Ultrasound therapy appears to be an effective treatment in reducing pain and improving functional capacity. NMES application has more effects on the muscle architecture.