Background: Heart rate variability (HRV) is an established, non-invasive parameter for the assessment of cardiac autonomic nervous activity and the health status in general cardiology. However, there are few studies on HRV in adults with congenital heart defects (CHDs). The aim of the present study was to evaluate the use of long-term continuous HRV measurement for the assessment of global health status in adults with cyanotic CHD. Methods: This prospective study included 45 adults (40% female, mean age = 35.2 ± 9.2 [range: 19–58] years) after cardiac surgical repair. HRV parameters were calculated from continuous 24 h measurements using a Bittium Faros 180 sensor (Bittium Corp., Oulu, Finland). Results: Postoperative patients with transposition of the great arteries (TGA) (n = 18) achieved significantly higher values of standard deviation of NN intervals (SDNN) (175.4 ± 59.9 ms vs. 133.5 ± 40.6 ms; p = 0.013) compared with patients with other conotruncal anomalies (n = 22). Comparing patients with TGA after a Senning–Brom or Mustard operation (n = 13) with all other heart surgery patients (n = 32), significantly higher HRV parameters were found after atrial switch (root mean square of successive RR interval differences: 53.6 ± 20.7 ms vs. 38.4 ± 18.3 ms; p = 0.019; SDNN: 183.5 ± 58.4 ms vs. 136.3 ± 45.3 ms; p = 0.006). A higher SDNN was also measured after Senning–Brom or Mustard operations than after a Rastelli operations (n = 2) (SDNN: 183.5 ± 58.4 ms vs. 84.5 ± 5.2 ms; p = 0.037). When comparing atrial switch operations (n = 3) with Rastelli operations, the SDNN value was significantly shorter in the Rastelli group (p = 0.004). Conclusions: Our results suggest that continuous HRV monitoring may serve as a marker of cardiac autonomic dysfunction in adults with cyanotic CHD after surgical repair. Impaired cardiac autonomic nervous activity may be associated with an increased risk of adverse reactions in patients with repaired CHD. Therefore, a longitudinal assessment of HRV patterns and trends may provide a deeper insight into dynamic changes in their autonomic regulation and disease progression, lifestyle changes, or treatments. As each person has individual variability in heart rate, HRV may be useful in assessing intra-individual disease progression and may help to improve personalized medicine. Further studies are needed to better understand the underlying mechanisms and to explore the full potential of HRV analysis to optimize medical care for ACHDs.