Focused low-intensity pulsed ultrasound(FLIPUS)and pulsed shortwave diathermy (PSWD) are presented as possible solution to attenuate the loss of function in the elderly with knee osteoarthritis(OA). The question remains unanswered which one is better modalities. The aim of this study was to compare the efficacy and safety of FLIPUS with PSWD in subjects with painful knee OA. In a prospective randomized trial,114 knee OA patients were randomly allocated to receive FLIPUS or PSWD therapy. The primary outcome was the change from baseline in the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) total and subscale scores. Secondary outcomes included numerical rating scale (NRS), Time Up and Go (TUG) test, active joint range of motion (ROM), and Global Rating of Change (GRC) scale. Data were collected at baseline, 12 days, 12 weeks and 24 weeks. Patients receiving FLIPUS therapy experienced significantly greater improvements in WOMAC total scores than patients receiving PSWD therapy at 12 days post-therapy (mean difference, -10.50; 95% CI, -13.54 to -7.45; P = 0.000). The results of the NRS scores, TUG test, ROM and GRC scale showed that participants treated with FLIPUS reported less pain and better physical function and health status than those treated with PSWD (P =0.011, P =0.005, P =0.025, P =0.011,respectively). Furthermore, patients in the FLIPUS group showed significant improvements in the WOMAC total scores and NRS scores at 12 and 24 weeks of follow-up (P =0.000 for all). FLIPUS immediately improved knee pain, dysfunction and health status compared with PSWD. In addition, the benefit of FLIPUS persists throughout follow-up. Trial registration: Chinese Clinical Trial Registry, ChiCTR2000032735. Registered 08/05/2020, http://www.chictr.org.cn/showproj.aspx? proj= 53413.