Among the types of blood cancers, non-Hodgkin lymphoma is the most common. The usual treatments for this type of cancer can cause heart failure. A descriptive observational study was conducted that included 16 non-Hodgkin lymphoma survivors and 16 healthy controls matched by age and sex. Vagal tone was evaluated in the short term with a three-channel Holter device, and the time and frequency domains were analyzed following a previously accepted methodology to evaluate cardiac autonomic balance. The results of the analysis revealed that the standard deviation of the NN interval (F = 6.25, p = 0.021) and the square root of the mean of the sum of the differences between NN intervals (F = 9.74, p = 0.004) were significantly higher in healthy subjects than in lymphoma survivors. In the heart rate variability (HRV) index, there were no significant differences between the groups (F = 0.03, p = 0.85), nor in the parameters of the frequency domains LF (F = 1.94, p = 0.17), HF (F = 0.35, p = 0.55), and the ratio LF/HF (F = 3.07, p = 0.09). HRV values were lower in non-Hodgkin lymphoma survivors in the first year after treatment, resulting in autonomic imbalance compared to healthy paired subjects.