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Abstract Background This study determined the effects of a novel combination of vitamin D and probiotic on metabolic and clinical symptoms in chronic schizophrenia. Methods This trial was conducted among 60 patients with chronic schizophrenia to receive either 50,000 IU vitamin D3 every 2 weeks plus 8 × 109 CFU/day probiotic (n = 30) or placebo (n = 30) for 12 weeks. Results Vitamin D and probiotic co-supplementation was associated with a significant improvement in the general (− 3.1 ± 4.7 vs. + 0.3 ± 3.9, P = 0.004) and total PANSS scores (− 7.4 ± 8.7 vs. -1.9 ± 7.5, P = 0.01). Vitamin D and probiotic co-supplementation also significantly increased total antioxidant capacity (+ 51.1 ± 129.7 vs. -20.7 ± 53.3 mmol/L, P = 0.007), and significantly decreased malondialdehyde (− 0.3 ± 0.9 vs. + 0.2 ± 0.4 μmol/L, P = 0.01) and high sensitivity C-reactive protein levels (− 2.3 ± 3.0 vs. -0.3 ± 0.8 mg/L, P = 0.001) compared with the placebo. Moreover, taking vitamin D plus probiotic significantly reduced fasting plasma glucose (− 7.0 ± 9.9 vs. -0.2 ± 9.9 mg/dL, P = 0.01), insulin concentrations (− 2.7 ± 2.3 vs. + 0.4 ± 2.0 μIU/mL, P < 0.001), homeostasis model of assessment-estimated insulin resistance (− 0.8 ± 0.7 vs. + 0.1 ± 0.7, P < 0.001), triglycerides (− 7.8 ± 25.2 vs. + 10.1 ± 30.8 mg/dL, P = 0.01) and total cholesterol levels (− 4.9 ± 15.0 vs. + 5.9 ± 19.5 mg/dL, P = 0.04) and total−/HDL-cholesterol ratio (− 0.1 ± 0.6 vs. + 0.3 ± 0.8, P = 0.04). Conclusion Probiotic and vitamin D for 12 weeks to chronic schizophrenia had beneficial effects on the general and total PANSS score, and metabolic profiles. Trial Registration This study was retrospectively registered in the Iranian website (www.irct.ir) for clinical trials registration (http://www.irct.ir: IRCT2017072333551N2). 07-31-2017 2