Clinical trials in men with biochemically recurrent prostate cancer (BRPC) have been hampered by long survival times, making overall survival (OS) a difficult end point to reach. Intermediate end points are needed in order to conduct such trials within a more feasible time frame. This is a retrospective analysis of 450 men with BRPC following prostatectomy treated at a single institution between 1981 and 2010, of which 140 developed subsequent metastases. Androgen deprivation therapy (ADT) was deferred until after the development of metastases. Cox regression models were developed to investigate factors influencing OS. Median metastasis-free survival (MFS) was 10.2 years 95% confidence interval (CI) 7.6–14.0 years; median OS after metastasis was 6.6 years (95%CI 5.8–8.4 years). Multivariable Cox regressions identified four independently prognostic variables for OS: MFS (HR 0.77; 95% CI 0.63–0.94), number of metastases (≤3 versus ≥4; HR 0.50; 95% CI 0.29–0.85), pain (absent versus present; HR 0.43; 95% CI 0.25–0.72), and bisphosphonate use (yes versus no; HR 0.60; 95% CI 0.37–0.98). MFS emerged as an independent predictor of OS in men with BRPC treated with deferred ADT after the development of metastases. MFS may be a reasonable intermediate end point in future clinical trials. This observation requires prospective validation.