Neurotrophic factors like Brain-Derived Neurotrophic Factor (BDNF), Neurotrophin 3 (NT3) and Nerve Growth Factor (NGF), play a role in neuroplasticity and neurogenesis contributing to the pathogenesis of schizophrenia. The objective of the present study was to investigate and compare the effect of olanzapine and lurasidone on the change in serum neurotrophins in patients with schizophrenia. The present study was a randomized, open-label, active-controlled, parallel design clinical trial. After randomization baseline evaluations of serum BDNF, NGF, NT3, Positive and Negative Syndrome Scale (PANSS) scoring, Social and Occupational Functioning Assessment Scale (SOFAS) scoring of 101 unmedicated schizophrenia patients were done. Patients were reassessed after 6 weeks of monotherapy with olanzapine or lurasidone. Serum BDNF increased after treatment with both the drug groups but rise with olanzapine was found to be significantly higher (916.22; 95 %CI: 866.07 to 966.37; p < 0.001) in comparison to lurasidone. Increase in levels NGF and NT3 was also observed but there was no significant difference between the groups (NGF: 2.32; CI: 3.54 to -3.53; p = 0.57 and NT3: 0.99; CI: 2.11 to 0.14; p = 0.086). The difference in improvement in PANSS and SOFASS with both the drugs was not statistically significant. Both the drugs alleviate the symptoms of schizophrenia but olanzapine was better tolerated. Our findings suggest that increase in serum BDNF with olanzapine monotherapy is significantly higher than that with lurasidone but there is no significant difference in change in serum NGF and NT3. TRIAL REGISTRATION: ClinicalTrials.gov identifier: (NCT03304457).