Aim: The effect of a web-based relapse prevention program might vary depending on a specific population if the study participants included drug users with various characteristics. This secondary analysis explored subgroups among Japanese drug users that may benefit from a web-based relapse prevention program. Methods: Outpatients with drug use disorder (n = 48) were randomly assigned to an 8-week, six-session web-based relapse prevention program (intervention group) or web-based self-monitoring only (control group). We tested the effects of the intervention on abstinence in different subgroups divided by a primary abused drug (methamphetamine vs other drugs), previous face-to-face relapse prevention (received vs not received), and outpatient treatment term (long-term: ≥3 years vs short-term: <3 years). Consecutive abstinence duration from the primary abused drug was compared in the subgroups, and the interaction between the intervention condition and the subgroup condition was assessed. Results: In the subgroup with short-term outpatient treatment, the intervention group maintained better abstinence than the control group. For those who used methamphetamine or those who had previously received a face-to-face relapse prevention program, the intervention group showed larger effect sizes than the results from all the participants. However, the interaction between the intervention condition and the subgroup condition was not significant for any subgroup. Conclusions: This study suggests that patients with short-term treatment may benefit from a web-based relapse prevention program as an alternative treatment. We need to recruit and allocate patients considering their treatment term in a future definitive trial.