Objective: To investigate whether an association exists between deceleration and acceleration areas on continuous fetal cardiotocography (CTG) and neonatal encephalopathy (NE). Design: A retrospective case-control study. Setting: A single tertiary medical center with over 15,000 births a year. Population: All deliveries complicated by neonatal encephalopathy in our center during the study period, with two controls for every case, matched by gestational age and cord blood pH. Methods: We compared CTG characteristics of low-risk pregnancies (35 weeks gestation or more), complicated by moderate to severe NE with matched controls. We analyzed the intrapartum CTG recordings by calculation of the deceleration and acceleration areas. Main outcome measure: Deceleration and acceleration areas and the ratio between the two. Results: During the period between 2013 and 2019, we identified 95 cases of low-risk pregnancies that were complicated by moderate to severe NE in our center. Thirty-three (34.7%) deliveries were excluded, mostly due to an insufficient duration of the CTG recordings. The remaining 62 cases were matched with 123 controls. We found that NE was significantly associated with an increased total deceleration area, a decreased total acceleration area and a lower acceleration-to-deceleration ratio. Conclusions: In our population, NE was significantly associated with increased total deceleration area, decreased total acceleration area and a lower acceleration-to-deceleration ratio, irrespective of cord blood pH. Development of a computerized real-time analysis of fetal heart rate tracings may contribute to making these measurements a more valid clinical tool.