Background Although there is considerable evidence that exercise improves the physical and mental health of individuals with schizophrenia, the most useful exercise technique for this population is still the subject of research. Purpose The aim of this study was to investigate the effects of Pilates exercises on functional capacity and mental health in individuals with schizophrenia. Methods Twenty-three participants were not randomly assigned to either Pilates exercise group (PEG) or nonspecific exercise group (NSEG). Ten participants from each group completed the study (87% response rate). The PEG participated in a 6-week Pilates exercise training twice per week, while the NSEG participated in a nonspecific activity program. 6-Minute Walk Distance (6-MWD) was assessed for functional capacity. Mental health was evaluated using Calgary Depression Scale for Schizophrenia (CDSS), and Brief Psychiatric Rating Scale (BPRS). Results 6-MWD significantly increased (p = .025), CDSS (p = .023) and BPRS (p = .012) scores significantly decreased in the PEG compared to baseline. Inter-group comparison showed that PEG had significantly better scores than NSEG in terms of the final 6-MWD (p = .005), CDSS (p = .008) and BPRS (p = .008). Conclusion Results showed that Pilates may help improve the functional capacity and mental health of individuals with schizophrenia, but the small sample size and methodological limitations limit the interpretability of this study.