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Objective The objective of this study was to determine the MCIDs for the numerical pain rating scale (NPRS), peak cough flow (PCF), peak expiratory flow (PEF), fatigue severity scale (FSS), and London chest activities of daily living scale (LCADL) in patients with SCI after rehabilitation. Methods Inpatients with SCI from two rehabilitation centres participating in a daily rehabilitation programme were recruited. The NPRS, PCF, PEF, FSS, and LCADL were collected at baseline and discharge. The global rating of change (GRC) scale was performed at discharge. MCIDs were calculated using anchor (linear regression, mean change and receiver operating characteristic curves) and distribution-based methods (0.5 times the baseline standard deviation, standard error of measurement (SEM), 1.96 times SEM, and minimal detectable change) and pooled using arithmetic weighted mean. Results Sixty inpatients with SCI (36 males; 54.5 (15.9) years) participated. On average their rehabilitation programme lasted 7.3 (1.7) weeks. Pooled MCID estimates were − 1.6 points for the NPRS, 69.8 L/min for the PCF, 77.4 L/min for the PEF, 1.1 points for the FSS, and 1.4 points for the LCADL. Conclusion Established MCIDs for NPRS, PCF, PEF, FSS, and LCADL will help health professionals to interpret results and guide rehabilitation interventions in patients with SCI.