Abstract Background Development of pharmaceutical interventions for schizophrenia emphasizes clinical efficacy and subsequent effectiveness and cost-effectiveness. However, given the many side effects of antipsychotic medication, it is important to consider the importance of different side effects on the preferences that people with schizophrenia have for different drugs. This study aims to use a discrete choice experiment to elicit patient preferences for antipsychotic medication with different side effects profiles. Method Preferences for antipsychotic side effects were investigated using a discrete choice experiment conducted in south London. 297 participants with a schizophrenia diagnosis who had been in receipt of anti-psychotic medication for a minimum of one month were included. Participants were presented with a sequence of choices involving five antipsychotic side effects (attributes) each with four levels. Conditional logit models were used to determine the side effects most (and least) likely to be preferred by people prescribed antipsychotics. Subgroup analyses explored the impact of side effects by gender, ethnicity, age, and symptoms. Results As expected, participants tended to value antipsychotic medications offering the least side effects, and the model coefficients were in the expected direction. For the whole sample and subgroups, memory and fatigue were the most important side effects, whereas palpations and mobility were the least important. Conclusions Participants had a strong preference for medications with the least side effects on memory and fatigue. These findings should inform drug development by pharmaceutical companies and prescribing practice by clinicians.