Improving the quality of teaching and learning, as well as school coexistence are international priorities for the new educational challenges of the 21st century (UNESCO 37 C/4 resolution). Physical Education (PE) has become a key subject for education on school coexistence by enabling significant motor experiences to promote interpersonal relationships and transform motor conflicts (MC). The objective of this research was to develop and validate two questionnaires (CONFLICT1-AGE and CONFLICT1-RES) to study secondary school students’ perception about MC in PE. Study 1 searched for evidence related to their content validity and response process validity, and Study 2 examined internal structure, reliability, and concurrent validity. As a result, a seven-item single-factor model was selected for CONFLICT1-AGE, and a five-item single-factor structure was chosen for CONFLICT1-RES. Both models exhibited an excellent fit to the data, where CONFLICT1-AGE: χ 2 (df) = 18.621 (14), p = 0.180, RMSEA (90% CI) = 0.033 0(0.000–0.069), CFI = 0.994, TLI = 0.991; CONFLICT1-RES: χ 2 (df) = 13.350 (5), p = 0.020, RMSEA (90% CI) = 0.075 (0.027–0.125), CFI = 0.986, TLI = 0.972. Furthermore, both questionnaires presented satisfactory internal consistency (αCONFLICT1-AGE = 0.745, αCONFLICT1-RES = 0.737). Their combination will provide a wide view of secondary school students’ perception about MC.