Suppression‐burst (SB) is an electroencephalographic pattern observed in neonatal‐ and infantile‐onset developmental and epileptic encephalopathies (DEEs), which are associated with high mortality in early life. However, the relation of SB electroencephalogram (SB‐EEG) with autonomic function requires clarification. We investigated the relationship between heart rate (HR) and phasic transition during SB‐EEG in DEEs to explore the mechanism of early death. Seven patients (two with KCNT1‐DEE) with neonatal‐ and infantile‐onset DEE who presented with SB‐EEG were retrospectively identified. Five‐minute SB‐EEGs were analyzed with simultaneous recording of electrocardiograms. Mean HR, suppression duration, and burst period were calculated by measuring RR intervals. Two patients with KCNT1‐DEE exhibited synchronous HR fluctuations, with an HR decrease during suppression and an increase during burst. The HR decrease was larger (−6.1% and −7.7%) and the median duration of suppression was longer (4.0 and 8.2 s) in patients with KCNT1‐DEE than the other five (range: −2.9% to 0.9% and 0.7‐1.7s, respectively). A strong negative correlation was confirmed between suppression duration and HR reduction rates in one patient with KCNT1‐DEE. SB phases may influence HR regulation in patients with KCTN1‐DEE.