BACKGROUND: Schizophrenia (SZ) is a chronic illness that is treated symptomatically. Cognitive dysfunction is a core feature of SZ that is relatively intractable to pharmacotherapy. Yoga can improve cognitive function among healthy individuals. A recent open trial indicated significant benefits of yoga training (YT) in conjunction with conventional pharmacotherapy among patients with SZ. AIMS: To describe the protocol for an ongoing randomised controlled trial designed to test whether the reported beneficial effects of YT on cognitive function among SZ patients can be replicated. Secondarily, the effects of YT on daily functioning living skills are evaluated. METHODS: Consenting patients with SZ receive routine clinical treatment and are randomised to adjunctive YT, adjunctive physical exercise (PE) or treatment as usual (proposed N = 234 total, N = 78 in each group). The trial involves YT or PE 5 days a week and lasts 3 weeks. Participants are evaluated thrice over 6 months. Cognitive functions measured by Trail Making Test, University of Pennsylvania Neurocognitive Computerised Battery were primary outcome measures while clinical severity and daily functioning measured by Independent Living Skills Survey were secondary outcome measures. RESULTS: A total of 309 participants have been randomised as of 31 August 2013, which exceeded beyond 294 proposed after attrition. Once participants begin YT or PE they generally complete the protocol. No injuries have been reported. CONCLUSIONS: Short term YT is feasible and acceptable to Indian SZ patients. If beneficial effects of YT are detected, it will provide a novel adjunctive cognitive remediation strategy for SZ patients.