The goal of this study was to investigate the association of physical activity (PA) and cardiorespiratory fitness with C-reactive protein (CRP) concentration in adolescents. The sample included 386 Portuguese adolescents (n = 207, female), age 12-18 years, assessed in the year 2012. The PA was assessed with the use of accelerometers, and the cardiorespiratory fitness was assessed by the Fitnessgram Pacer test. Blood samples were collected after a 10-hour fasting, and high-sensitivity PCR concentration was further assessed. Significant associations between CRP and cardiorespiratory fitness were found for females (r = -0.313; p < 0.001) and males (r = -0.163; p < 0.05); however, when adjusted by the BMI, the associations remained significant only for females (r = -0.215; p < 0.001). Regarding the association between CRP and PA, no significant associations were found for both genders. Therefore, CRP is apparently negatively associated with cardiorespiratory fitness, with differences between males and females; for females it seems less dependent than BMI.