Fetal heart rate (FHR) monitoring is commonly used although clinical studies questioned its diagnostic value. Sophisticated FHR variability (fHRV) measures such as fHRV complexity may improve the sensitivity and specificity of FHR monitoring. A more detailed understanding of the physiology underlying fHRV complexity is essential to harness its use for monitoring fetal health. To examine the specific effects of vagal and sympathetic modulations on fHRV complexity, we blocked vagal activity with atropine and sympathetic activity with propranolol in near-term fetal sheep (n = 7, 0.85 gestation). Under these conditions, we analyzed the linear and nonlinear parts of fHRV complexity from autonomic information flow. Overall fHRV complexity decreased with both drugs compared with NREM sleep baseline (P < 0.05). With atropine, this was due to a decrease of the linear part of fHRV complexity on the long term time scale (P < 0.05) suggesting that vagal modulation of fHRV is adequately described by linear fHRV measures. With propranolol, the nonlinear part of fHRV complexity decreased on the short-term time scale decreased (P < 0.05) suggesting that sympathetic influences on fHRV can be detected by the nonlinear part of fHRV complexity. Thus, the complex interplay of vagal and sympathetic modulations of fHRV is reflected differently and specifically in the linear and nonlinear properties of fHRV complexity, and on different time scales. Analysis of linear and nonlinear properties of fHRV may improve sensitivity and specificity of FHR health monitoring.