Isaac was a son of Manuel Comnenus (Manuel I Comnenus), an officer of the Byzantine emperor Basil II. On his deathbed, Manuel commended Isaac and his other son, John, to the emperor's care. After having them educated, Basil advanced them to high positions. Isaac, by his prudent conduct in protecting the peoples of the empire, won the confidence of the army during the reigns of Basil's successors.

In 1057 Isaac entered into a military plot to depose the emperor Michael VI (Michael VI Stratioticus), and in June of that year Isaac was proclaimed emperor in Paphlagonia in Asia Minor. The rebels marched on Constantinople, captured Nicaea (now İznik, Turkey), and defeated Michael's forces at Petroë on August 20. Michael abdicated on August 31, and Isaac was crowned emperor the following day.

Although the patriarch Michael I Cerularius (Michael Cerularius) had helped bring Isaac to power, the two men soon quarreled over Isaac's stringent financial policies, including the confiscation of some church property, and over the patriarch's attempt to subordinate civil power to the church. Isaac demanded that Cerularius resign, and when the patriarch refused, the emperor had him arrested and exiled (1058). Cerularius was charged with treason and heresy but died before his trial could take place.

In the spring of 1059 Isaac led a military expedition against the Hungarians, and in the summer of that year he fought against the Pechenegs, who were ravaging the northern frontiers. In November 1059 he became ill. Believing his illness to be mortal, he abdicated (December 25, 1059) and appointed as his successor Constantine X Ducas. Although he recovered, Isaac did not resume his throne but retired to a monastery, where he spent the remaining two years of his life as a monk, alternating menial offices with literary studies.