Background Schizophrenia is one of the most burdensome psychiatric disorders. Novel neuromodulatory techniques including cathodal transcranial direct current stimulation (c-tDCS) and continuous theta burst stimulation (cTBS) using repetitive transcranial magnetic stimulation (rTMS) are increasingly being used in alleviating the auditory verbal hallucinations that are persisting despite adequate antipsychotic treatment. Brain connectivity modulation by stimulating the left temporoparietal junction is thought to mediate these effects. The differential neurobiological mechanisms and efficacy of these two neuromodulation techniques are not known. We are unaware of any systematic studies that can guide clinicians in choosing between the two techniques. This protocol describes a parallel-arm, double-blind, randomized cross-over study to identify resting brain functional connectivity markers of response to cTBS and c-tDCS persistent auditory hallucinations to improve the efficacy of interventions. Methods Two hundred and ten consenting patients with schizophrenia with persistent auditory hallucinations will be randomly assigned to receive 15 days (30 sessions) of c-tDCS+sham-TBS or sham-tDCS+cTBS over the left temporoparietal region at three study centres. After a gap of 2-4 weeks, non-responders to the intervention will cross-over to the other arm. Clinical assessments, neurocognitive assessments, and multimodal investigations (magnetic resonance imaging, electroencephalography, heart rate variability, investigative transcranial magnetic stimulation-transcranial direct current stimulation, gene polymorphisms) will be conducted at baseline and repeated after the end of both phases of the trial. A differential pre-treatment resting brain functional connectivity signal will identify responders to cTBS or c-tDCS. Registration Clinical Trial Registry of India (CTRI/2021/05/033783) registered on 25/05/2021.