We aimed to assess the individual and joint association of serum vitamin D and cardiorespiratory fitness (CRF) with obesity and metabolic syndrome (MetSyn). In this cross-sectional study 270 adults with an age range of 18 years and older were recruited from health centers from five districts in Tehran, Iran. CRF was assessed with Bruce protocol. MetSyn was defined based on International Diabetes Federation 2009. The odds ratio (OR) and 95 % confidence interval (CI) of obesity and MetSyn across tertiles of serum vitamin D and CRF were estimated with control for confounders. The results indicated that neither 25(OH)D nor 1,25(OH)D was associated with obesity and MetSyn. There was a strong inverse association between CRF and general (P
-trend < 0.001) and abdominal adiposity (P
-trend: 0.001). The joint association of vitamin D and CRF indicated that the inverse association of CRF with obesity was stronger in those with high serum vitamin D than those with low serum vitamin D and this joint association remained after considering age and diet quality. There was a significant inverse association for those with low serum 25(OH)D and high CRF (OR: 0.12, 95 % CI: 0.04–0.81; P = 0.02) compared to those with low serum 25(OH)D and low CRF in the crude model. Also, the OR of general obesity was 0.17 (95 % CI: 0.02–0.79; P = 0.03) for those with high CRF and low serum 1,25(OH)D compare with the reference group. Our findings indicated a strong inverse association between CRF and obesity, especially in those with high serum vitamin D.