Introduction: Musculoskeletal injuries (MSK-I) are among the most common contributors of disabilities worldwide. Aircrew given their charter of duties have a higher risk of developing MSK-I. Functional assessment of aircrew after recovery is conducted at the Institute of Aerospace Medicine (IAM) Bengaluru. The maneuvers utilized in the present assessment lack objectivity and scorability. Hence, this study aimed at establishing an exercise maneuver protocol (EMP), henceforth referred to as IAM-EMP, which could overcome the existing shortcomings. Material and Methods: 202 age-matched aircrew (180 males/ 22 females) were selected and classified into control (100 healthy aircrew) and experimental (102 aircrew with MSK-I) groups. All aircrew underwent the complete human engineering (HE) assessment. In addition, Functional Movement Screen™ (FMS™) was carried out. Jump test was added to FMS™ after defining its scorability criteria to form the IAM-EMP. EMP was scored on a scale of 0-24. The scores were compiled and analyzed. Results: Descriptive analysis showed comparable male and female FMS™ and EMP Scores. Cutoff scores of FMS™ and EMP for the study population were defined using receiver operating characteristic curve analysis. Area under the curve for EMP was found to be statistically better than FMS™ (P < 0.05) in predicting fitness of an aircrew keeping complete HE assessment as gold standard. EMP was validated on randomly selected 50 aircrew (25 from each group). Conclusion: IAM-EMP is an objective and scorable tool which can be used on both male and female aircrew between 18 and 45 years of age for their functional assessment post recovery from an MSK-I. Incorporation of the tool with other components of HE assessment would improve the yield of overall evaluation.