Background Advances in mobile health (mHealth) have enabled systematic and continuous management of patients with chronic diseases. Objective We developed a smartphone-based mHealth system and aimed to evaluate its effects on health behavior management and risk factor control in stroke patients. Methods With a multifaceted stroke aftercare management system that included exercise, medication, and educational materials, we performed a 12-week single-arm intervention among eligible poststroke patients in the stroke clinic from September to December 2016. The intervention consisted of (1) regular blood pressure (BP), blood glucose, and physical activity measurements; (2) stroke education; (3) an exercise program; (4) a medication program; and (5) feedback on reviewing of records by clinicians. Clinical assessments consisted of the stroke awareness score, Beck Depression Inventory-II (BDI), EuroQol-5 Dimensions (EQ-5D), and BP at visit 1 (baseline), visit 2 (4 weeks), and visit 3 (12 weeks). Temporal differences in the parameters over 12 weeks were investigated with repeated-measures analysis of variance. Changes in medication adherence at visit 1-2 (from visit 1 to visit 2) and visit 2-3 (from visit 2 to visit 3) were compared. System satisfaction was evaluated with a self-questionnaire using a 5-point Likert scale at visit 3. Results The study was approved by the Institutional Review Board in September 2016, and participants were enrolled from September to December 2016. Among the 110 patients enrolled for the study, 99 were included in our analyses. The mean stroke awareness score (baseline: 59.6 [SD 18.1]; 4 weeks: 67.6 [SD 16.0], P<.001; 12 weeks: 74.7 [SD 14.0], P<.001) and BDI score (baseline: 12.7 [SD 10.1]; 4 weeks: 11.2 [SD 10.2], P=.01; 12 weeks: 10.7 [SD 10.2], P<.001) showed gradual improvement; however, no significant differences were found in the mean EQ-5D score (baseline: 0.66 [SD 0.33]; 4 weeks: 0.69 [SD 0.34], P=.01; 12 weeks: 0.69 [SD 0.34], P<.001). Twenty-six patients who had uncontrolled BP at baseline had −13.92 mmHg (P=.001) and −6.19 mmHg (P<.001) reductions on average in systolic and diastolic BP, respectively, without any antihypertensive medication change. Medication compliance was better at visit 2-3 (60.9% [SD 37.2%]) than at visit 1-2 (47.8% [SD 38.7%], P<.001). Conclusions Awareness of stroke, depression, and BP was enhanced when using the smartphone-based mHealth system. Emerging mHealth techniques have potential as new nonpharmacological secondary prevention methods because of their ubiquitous access, near real-time responsiveness, and comparatively lower cost.