Background: Job crafting, an employee-initiated job design/redesign, has become important for employees' well-being such as work engagement. This study examined the effectiveness of a newly developed job crafting intervention program on work engagement (as primary outcome), as well as job crafting and psychological distress (as secondary outcomes), using a pretest-posttest study design among Japanese employees. Methods: Participants were managers of a private company and a private psychiatric hospital in Japan. The job crafting intervention program consisted of two 120-min sessions with a two-week interval between them. Outcomes were assessed at baseline (Time 1), post-intervention (Time 2), and a one-month follow-up (Time 3). The mixed growth model analyses were conducted using time (Time 1, Time 2, and Time 3) as an indicator of intervention effect. Effect sizes were calculated using Cohen's d. Results: The program showed a significant positive effect on work engagement (t = 2.20, p = 0.03) in the mixed growth model analyses, but with only small effect sizes (Cohen's d = 0.33 at Time 2 and 0.26 at Time 3). The program also significantly improved job crafting (t = 2.36, p = 0.02: Cohen's d = 0.36 at Time 2 and 0.47 at Time 3) and reduced psychological distress (t = -2.06, p = 0.04: Cohen's d = -0.15 at Time 2 and -0.31 at Time 3). Conclusions: The study indicated that the newly developed job crafting intervention program was effective in increasing work engagement, as well as in improving job crafting and decreasing psychological distress, among Japanese managers. Trial registration: UMIN Clinical Trials Registry UMIN000024062. Retrospectively registered 15 September 2016.