Though Pratap Manikya is stated in the Rajmala to be a son of Dharma Manikya I,^[3] later scholarship proved this to be chronologically improbable.^[4] It is instead believed that he was Dharma's grandson, with his father being Ratna Manikya I.^[5] There were also uncertainties regarding the years of Pratap's rule. A coin supposedly minted during his reign bears the year Saka 1412 (1490 CE), though the modern-style script has led to doubts regarding its authenticity.^[6] It is notable that Pratap's immediate successors struck coins in 1488 and 1489 respectively.^[5]

A younger son of his father, Pratap's rule had been propped up by the support of prominent army generals in opposition to his elder brother Dhanya, against whom he waged a civil war.^[7] According to the Rajmala, because of his impiety, Pratap soon lost the support of these nobles, who launched a conspiracy against him. The chronicle continues that due to his formidable physical strength and stoutness, Pratap had to be killed at night while he slept.^[8]

He was succeeded in quick succession by the minor Vijaya Manikya (who may have been his son)^[1] and Pratap's younger brother Mukut, before the throne finally settled on Dhanya, whose long reign lasted until 1515.^[9]