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Abstract Background It has been reported that cyclosporine A (CYA) treatment may benefit idiopathic pulmonary fibrosis (IPF) patients. We conducted a randomized, controlled trial at 27 centers across Japan to evaluate the efficacy and safety of CYA with low-dose corticosteroids (CS) for IPF treatment. We compared these findings with others obtained using cyclophosphamide (CPA) combined with low-dose CS: the current standard therapy for IPF. Methods The study involved patients between 50 and 74 years of age with well-defined IPF. The primary endpoint was a change in forced vital capacity (FVC) between baseline and 48 weeks. Results We started this trial in May 2005 and ended it in December 2008. Ninety-nine patients were enrolled in the study. There was no significant difference between the CYA and CPA groups with regard to the change in FVC between baseline and 48 weeks (−0.078 L and −0.087 L, respectively). Neither did the two groups differ significantly with regard to the incidence rates of several adverse events. Conclusions This clinical trial revealed no significant differences between the CYA group and the CPA group with regard to either safety data or the primary endpoint. However, the trial should be regarded as inconclusive because of its small sample size. There was a trend toward a reduction in FVC decline per year when the trial groups were compared with the placebo groups of previous studies, despite patients in this study having severely impaired lung function. Both therapies were well tolerated and lacked serious adverse effects.