The aim of this study is to investigate the effect of inquiry-based instruction in the teaching of fundamental movement skills to fifth-grade students on the children's perceived motor competence. Utilizing a post-test experimental design with control group, the study was carried out with 260 fifth-grade students studying in ten different classes at five different schools located in the city centre of Manisa during the 2019-2020 academic year. For collection of the data, the "Perceived Motor Competence Questionnaire in Childhood" (PMC-C), and a "Personal Information Form" (PIF) developed by the researchers, were used. To test the effectiveness of the quasi-experimental process in the post-test design with control group, t-test was used. In the inquiry-based instruction in the teaching of fundamental movement skills of the students, a statistically significant difference was found in favour of the experimental group in the subscales of perceived motor competence. Regarding the gender variable of the students, a statistically significant difference was found between female and male students in favour of boys in the subscales of fundamental motor skills. In conclusion, it can be said that the inquiry-based instructional model was more effective than the direct instructional model in developing the fundamental motor skills of "locomotor skills" and "object control skills". Moreover, when evaluated in terms of gender, male students benefited more from the inquiry-based instructional model in terms of "object control skills".