The aim of this study was to examine the associations of objectively measured physical activity (PA) and cardiorespiratory fitness (CRF) with different continuous metabolic syndrome (MetS) scores in adolescents. A cross-sectional sub-sample of 202 adolescents (99 girls), aged 13-17 years, were selected from the AFINOS Study. Body mass index, sum of 6 skindfold, waist circumference, systolic and diastolic blood pressure, insulin, glucose, triacylglycerol, and HDL-cholesterol levels were determined. Moderate PA (MPA), vigorous PA (VPA) and moderate to vigorous PA (MVPA) were assessed by the ActiGraph accelerometer for 7 consecutive days and CRF was estimated by the 20-m shuttle run test. Three continuous MetS scores were calculated according to the methodology of the Corpus Christi Child Heart Study (CCCHS), the Aerobic Center Longitudinal Study (ACLS), and the European Youth Heart Study (EYHS). VPA and MVPA were significantly related with CRF. Only CRF, and not patterns of PA, was inversely and independently associated with the three MetS scores although with different magnitudes (ranged: beta = 0.22 to 0.36, p < 0.05). A significant VPA x CRF interaction (p = 0.011) was found using the ACLS MetS score. Trends across VPA-CRF groups were significantly different with ACLS and EYHS (p = 0.002 and p = 0.006, respectively), but not with CCCHS (p = 0.313) continuous MetS scores. These findings support the key role of CRF on the MetS and the relevance of PA, especially VPA, to provide CRF in adolescents. A unified pediatric definition of MetS might minimize the discrepancies among studies.