Dorojatun was born on 12 April 1912 in Yogyakarta. His father was Prince Haryo Puruboyo, a son of the reigning Sultan, and his mother was Raden Ayu Kustilah, who received the title of Kangjeng Raden Ayu Adipati Anom in 1915. She was the daughter of Prince Mangkubumi, who was a brother of, and an influential adviser to, the Sultan, Hamengku Buwono VII. The Sultan paid a formal visit to congratulate Puruboyo, and paid him a special allowance in honour of the event.

Dorojatun's mother was Puruboyo's official wife, and they had been married for four years. When her husband unexpectedly became next in line to become Sultan not long after Dorojatun's birth, she had good prospects of becoming permaisuri (queen) in due course. But at the time this was in the future. Hamengku Buwono VII, although already in his seventies, seemed perfectly healthy and might live some years yet.

Prince Puruboyo became Sultan by accident. He was the fourth son of the monarch, but two of his elder brothers died relatively young and one was mentally unfit. One of the first two, Hamengkunagoro, had lived long enough to marry and be named crown prince, but he died in 1913 at the age of 35 before he could become Sultan. Puruboyo consequently became crown prince in his turn on 21 July 1914, when Dorojatun was two years old. From this time on, as the first and only son born to Puruboyo and his official wife, he was regarded as a likely future Sultan. His four elder brothers were not expected to succeed to the throne because their mothers were minor wives of Prince Puruboyo.

When an important ruler is born in Java, a sign from heaven is usually expected, such as lightning, earthquakes, or volcanic eruptions. But the senior retainers of the palace admitted in later years that no extraordinary events accompanied Dorojatun's birth. This did not prevent stories emerging much later that such omens had occurred, especially from those who believed that Hamengku Buwono IX had something of the Ratu Adil (Just King) about him.

He was known formally as Gusti Raden Mas Dorojatun, although he carried the Dutch-style nickname of Henkie in his early years, after the husband of the reigning Dutch Queen Wilhelmina. Javanese princes often bore European nicknames at the time.