Jake was born in 2355 to Jennifer Sisko, who was killed in 2367 during the Battle of Wolf 359, when Benjamin Sisko served aboard the USS Saratoga. In 2369, he reluctantly moved with his father to space-station Deep Space Nine.
Jake soon becomes friends with a Ferengi named Nog , son of Rom , despite the disapproval of both of their fathers. Jake and Nog become the first students to enroll in Keiko O'Brien's school. When Rom pulls Nog out of school, Jake secretly tutors him. The pair also briefly form the "No-Jay Consortium" as a front for their business schemes.
Jake aspires to be a writer, though he declines a scholarship to the Pennington School (New Zealand) in 2371. He briefly dates a Bajoran dabo girl named Mardah, against his father's approval, who embarrasses Jake by revealing his penchant for dom-jot hustling and poetry to his father. In 2372, Jake writes a draft of his first novel, "Anslem" under the influence of Onaya, an alluring alien woman who feeds on creative neural energy by tactile absorption through the cranium
As Jake was becoming a young adult, and feeling the need for independence, he moves out of his father's quarters to become roommates with Nog, who is now a Starfleet Academy cadet on DS9 for field study. Jake's slovenliness and Nog's new-found neatness initially strain their friendship, until Benjamin Sisko, as Nog's commander and Jake's father, orders them to settle their differences.
Jake is responsible for introducing his father to Kasidy Yates , a freighter captain. The elder Sisko would become romantically involved with Yates, and would eventually marry in the closing months of the Dominion War. During the Dominion occupation of Deep Space Nine, Jake remains there and serves as a reporter for the Federation News Service, though most of his work is suppressed by Weyoun and the Dominion authorities. Nevertheless, he is able to secretly send messages to his father through Morn.