Background: To compare the effects of high-intensity interval training (HIIT) alone vs. HIIT combined with L-citrulline (CIT) supplementation on functional capacity and muscle function in dynapenic-obese elderly. Methods: A total of 56 obese (fat mass: men > 25%, women > 35%) and dynapenic (grip strength/body weight: women < 0.44, men < 0.61) subjects were recruited and divided in two groups: HIIT+CIT (n = 26; age: 6 5 ± four years) vs. HIIT+Placebo (PLA, n = 30; age: 68 ± four years). Participants followed a 12-week HIIT using an elliptical trainer. Participants took a single and isocaloric 10 g-dose of CIT or PLA every day. Body composition; functional and aerobic capacities; absolute or relative upper and lower limbs muscle strength, muscle power; and energy balance were measured pre and post intervention. Results: Both groups significantly improved functional capacity and muscle function. However, HIIT+CIT demonstrated greater improvements in fast-paced Timed Up & Go (p = 0.04) and upper limbs muscle strength (absolute and relative) (p = 0.05) than HIIT+Placebo. Conclusion: CIT supplementation when combined with HIIT seems to induce greater improvements in upper limbs muscle strength and walking speed in dynapenic-obese elderly. Further studies are needed to confirm our results, to elucidate the mechanisms underlying the beneficial effects of CIT and to define the long-term impact of CIT/HIIT.