The purpose of this study is to examine the effect of the inquired-based learning model used in the physical fitness unit of the physical education and sports course, in middle school, on the level of physical fitness knowledge. A total of 126 students participated in the study as intervention (n = 63) and control (n = 63) groups in the physical education and sports course in the fifth grade. Herein, the physical fitness knowledge levels were obtained by using the “health-related fitness knowledge Test for Turkish middle school students” (HRFKT) developed by Hünük and İnce (2010). Lessons were conducted simultaneously using the inquired-based learning and direct teaching models, in intervention and control groups. The effect of the inquired-based learning model on physical fitness knowledge levels was analyzed using a 2 (Time: before or after intervention) x 2 (Group: intervention l or control) analysis of variance (ANOVA) for mixed measures. Additionally, partial eta-square (η2) was calculated to determine the effect size. The findings indicate that the physical fitness knowledge levels of the inquired-based learning model increased statistically significantly (F [1_125] = 61.595, p < .05) compared to the direct teaching model. As a result, the students trained with the inquired-based learning model learned the concepts of physical fitness by experiencing the steps of producing scientific knowledge, observing the changes in the body during exercise, and using the scientific thinking method.