The purpose of this study was to examine the relationship between cardiac autonomic control derived from heart rate variability (HRV), high-sensitivity C-reactive protein (hs-CRP) and physical activity (PA) levels measured using accelerometers. A total of 80 healthy university students volunteered to participate in this study (20.56 ± 0.82 years, 1.36 ± 1.5 mg/L of hs-CRP). The participants were divided into groups based on tertiles of hs-CRP. Analysis of covariance adjusted to PA was used to assess group differences in HRV. Associations between hs-CRP, HRV indices and PA were analyzed using Pearson's correlation. The participants at the highest tertile of hs-CRP (tertile 3) had lower cardiac vagal modulation (SDNN, tertile 1=78.05 ± 5.9,tertile 2=82.43 ± 5.9,tertile 3=56.03 ± 6.1; SD1, tertile 1=61.27 ± 5.3, tertile 2=62.93 ± 5.4, tertile 3=40.03 ± 5.5). In addition, vagal indices were inversely correlated with hs-CRP but positively correlated with PA (SDNN r=−0.320, SD1 r=−0.377; SDNN r=0.304, SD1 r=0.299; P<0.05). Furthermore, the most physically active subjects had lower levels of hs-CRP and the highest levels of vagal modulation.