The aims of this study were to investigate the efficacy of heart rate variability biofeedback (HRVBFB) intervention in terms of reducing craving, severity of dependence, and rate of positive methamphetamine urine testing in men taking part in a methamphetamine use disorder outpatient treatment program. Sixty-one adult men received either HRVBFB treatment plus treatment as usual (TAU) over four weeks or TAU only. Men receiving HRVBFB showed significantly greater reductions in craving, dependence severity, and the rate of positive methamphetamine urine testing at the end of the intervention and four weeks of follow-up. The analyses further showed that the levels of craving and dependence severity at treatment entry were predictive of changes in craving and dependence severity at the end of treatment and follow-up, respectively. The baseline status of a positive methamphetamine urine test only predicted a positive methamphetamine urine test at the end of treatment, not at the end of the follow-up period. Our results showed HRVBFB intervention has merits as an adjunct treatment to ameliorate cravings and reduce the severity of dependence experienced by persons with methamphetamine use disorder. An added value of HRVBFB intervention is the fact that it can be easily and affordably implemented in everyday life.