Heraclius died in Constantinople on [[February 11]], 641. He was succeeded by his sons Constantine III and Heraklonas.

Between his two wives, Heraclius sired at least twelve children. Of these, two from his second marriage to Martina are known to be handicapped, seen at the time as punishment for his illegal marriage. He had at least one illegitimate son, Atalarichos. Atalarichos participated in a plot with his cousin the magister Theodorus and an Armenian noble Davis Saharuni against Heraclius. After the plot failed in 637 Atalarichos was mutilated and exiled. When Heraclius learned in his last years of life of the struggle between his son Heraclius Constantine and his wife Martina in which she was trying to position her son Heraklonas in line to the throne, Heraclius wrote his will making both Heraclius Constantine and Heraklonas his joint successors with Martina as Empress.

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