Background Mobile health (mHealth) interventions, a more cost-effective approach compared with traditional methods of delivering lifestyle coaching in person, have been shown to improve physical parameters and lifestyle behavior among overweight populations. In Japan, the Specific Health Checkups and Specific Health Guidance (SHG) started in 2008 to treat obesity and abdominal obesity. However, the effectiveness of SHG is limited owing to its in-person counseling. The effect of mHealth on SHG has yet to be demonstrated. Objective This study aims to determine whether a mobile self-management app (DialBeticsLite) could make the SHG more beneficial among patients with abdominal obesity to achieve a reduction in visceral fat area (VFA). Methods This study was an open-label, 2-arm, parallel-design randomized controlled trial. We recruited 122 people in September 2017 and randomly assigned them into either the intervention or control group. All participants attended an educational group session that delivered information regarding diet and exercise. In addition, participants in the intervention group were asked to use DialBeticsLite for 3 months. DialBeticsLite facilitated the daily recording of several physical parameters and lifestyle behavior and provided feedback to encourage an improvement in behavior. The primary outcome was the change in VFA from baseline to the 3-month follow-up. Secondary outcomes included changes in both physical and metabolic parameters from baseline to the 3-month follow-up. The Welch 2-tailed t test was conducted to analyze the effects of DialBeticsLite on both the primary and secondary outcomes. Results Of the 122 participants recruited, 75 (61.5%) were analyzed because 47 (38.5%) were excluded: 37 (30.3%) because of ineligibility and 10 (8.2%) because of withdrawal of consent. The mean age was 49.3 (SD 6.1) years in the intervention group (41/75, 55%) and 48.5 (SD 5.3) years in the control group (34/75, 45%), and all participants were men, although unintentionally. The baseline characteristics did not differ significantly between the intervention and control groups, except for VFA. The average change of VFA was −23.5 (SD 20.6) cm2 in the intervention group and +1.9 (SD 16.2) cm2 in the control group (P<.001). Statistically significant differences were also found for the change of body weight, BMI, and waist circumference. These findings did not change after adjusting for VFA at the baseline. The intervention had no significant effect on any of the metabolic parameters. An exploratory analysis showed significant associations between the change in VFA and steps per day and between the change in VFA and calorie intake per day within the intervention group. Conclusions Our findings indicate that an mHealth intervention facilitating the daily monitoring of several physical parameters and lifestyle behavior can be highly effective in inducing visceral fat loss and weight loss among adults eligible for SHG. Trial Registration UMIN Clinical Trials Registry UMIN000042045; https://tinyurl.com/4vat3v53