The effects of resistance training (RT) combined with whole-body vibration (WBV) on muscle fitness, particularly muscle hypertrophy and neuromuscular performance, are not well understood. We investigated the effects of WBV in healthy, untrained participants after a 13-week RT course by performing magnetic resonance imaging and by measuring maximal isometric (with electromyography) and isokinetic knee extension strengths, isometric lumbar extension torque, countermovement-jump, knee extension endurance, and sit-ups. Thirty-two individuals (22–49 years old) were randomly assigned to RT groups with (RT-WBV, n=16) or without WBV (RT, n=16). Following the RT course, significantly higher increases in the cross-sectional areas of m. psoas major (vs baseline values) and erector spinae muscle (vs the RT group) were observed in the RT-WBV group (+10.7%, P<0.05; +8.7%, P<0.05) compared with the RT group (+3.8%, P=0.045; 0.0%). Higher increases from baseline were also observed in maximal isometric force, concentric knee extension torque, countermovement-jump, and maximal isometric lumbar extension torque in RT-WBV (+63.5%; +76.7%, +15.0%, and +51.5%, respectively; P<0.05) than in those of RT (+25.6%, P=0.001; +17.8%, P=0.18; +11.3%, P=0.001; and +26.4%, P<0.001, respectively). The WBV-induced increases in muscle hypertrophy and isometric lumbar extension torque suggest a potential benefit of incorporating WBV into slow-velocity RT programs involving exercises of long duration.