Background: Military populations, including fast jet aircrew (FJA - aka fighter aircrew/pilots), commonly suffer from musculoskeletal complaints, which reduce performance and operational capability. Valid surveillance tools and agreed recordable injury definitions are lacking. Our objective was to develop and then evaluate the validity of a musculoskeletal complaints surveillance and monitoring tool for FJA. Methods: A Delphi study with international experts sought consensus on recordable injury definitions and important content for use in a surveillance and monitoring tool for FJA. Using these results and feedback from end-users (FJA), the University of Canberra Fast Jet Aircrew Musculoskeletal Questionnaire (UC-FJAMQ) was developed. Following its use with 306 Royal Australian Air Force (RAAF) FJA over 4 × five-month reporting periods, validity of the UC-FJAMQ was evaluated via multi-level factor analysis (MFA) and compared with routine methods of injury surveillance. Results: Consensus was achieved for: eight words/descriptors for defining a musculoskeletal complaint; six definitions of recordable injury; and 14 domains important for determining overall severity. The UC-FJAMQ was developed and refined. MFA identified three distinct dimensions within the 11 items used to determine severity: operational capability, symptoms, and care-seeking. MFA further highlighted that symptom severity and seeking medical attention were poor indicators of the impact musculoskeletal complaints have upon operational capability. One hundred and fifty-two episodes of time loss were identified, with the UC-FJAMQ identifying 79% of these, while routine methods identified 49%. Despite modest weekly reporting rates (61%), the UC-FJAMQ outperformed routine surveillance methods. Conclusions: The UC-FJAMQ was developed to specifically address the complexities of injury surveillance with FJA, which are similar to those noted in other military and sporting populations. The results demonstrated the UC-FJAMQ to be sensitive and valid within a large group of FJA over 4 × five-month reporting periods. Adoption of consistent, sensitive, and valid surveillance methods will strengthen the FJA injury prevention literature, ultimately enhancing their health, performance, and operational capability.