Chakotay, son of Koloplak, was born on Trebus in 2329. By the age of 6, Chakotay wanted to go against his family traditions and be a paleontologist. (VOY novel: Pathways and episode: "One Small Step").
Young Chakotay also had an independent nature, and often went exploring on Trebus. In 2341, Chakotay raided a junkyard on the planet and became trapped in the wreckage of an old runabout, fortuntately he was later rescued. (VOY episode: "Equinox, Part I").
Despite his independent nature, in 2344 and 2345, Chakotay accompanied his father to Central America on Earth to visit the homelands of their ancestors. During his time their Chakotay learns of the Sky Spirits and begins to respect his cultural heritage. (VOY novel: Pathways and episode: "Tattoo").
In 2345, 15-year-old Chakotay was seriously considering entering Starfleet, and often spent time around the Starfleet personnel on the planet, led by Captain Demora Sulu. Sulu sponsored Chakotay's applications into the Academy, but Chakotay had to lie to his father and state that Captain Sulu was a man in order to protect his feelings. (VOY short story: "Seduced", Tales from the Captain's Table).
- Note: The novel Pathways suggest that Chakotay's entrance into the Academy was sponsored by Hiromi Sulu, grandson of Hikaru Sulu, while other sources suggest that it was Hikaru himself that sponsored him, or even Hikaru's daughter Demora Sulu. 
Thanks to the sponsorship of Captain Sulu, Chakotay entered Starfleet Academy in late 2347. During his first few weeks at the Academy he became friends with Svetlana "Sveta" Korepanova from Ekaterinburg, Russia. He also became unlikely friends with his late-assigned roommate, an unflappably cheerful Bolian named Chert.
At the end of his first year at the Academy, Chakotay considered leaving, and returned to Trebus to undergo his first vision quest using the akoonah. As a result of his vision quest he decided to continue his Academy education.
During his first year at the Academy, Chakotay underwent intensive pilot training in North America. Shortly after, Chakotay underwent training on Venus, and later underwent training for a semester in the asteroid belt located between Mars and Jupiter. (VOY episodes: "Future's End, Part II" and "Blink of an Eye").
Also during his time at the Academy, Chakotay became a proficient light-heavyweight boxer, and scored a record of 23 wins and only one loss, which was to a Nausicaan. (VOY episodes: "The Fight" and "Tsunkatse").
Chakotay graduated from the Academy in 2351. By 2353 he served aboard the USS Vico, as an aide to Captain Roger Hackney and held the rank of lieutenant. It was aboard the Vico that Chakotay had his first encounter with a Cardassian warship that had violated the Federation border. (VOY novel: Pathways)
At some point, Chakotay began serving on the USS Heritage. A female officer named Grant was the first officer. During this time, Chakotay and Grant begun a romantic relationship, one which Grant noted in Chakotay's Starfleet file. In 2375, the crew of the USS Voyager held a "roast" of Chakotay for his birthday. Parts of his Starfleet record were read aloud, including Grant's note about their relationship. (VOY short story: "Isabo's Shirt")
In 2362, Chakotay transferred to the USS Gage. He stayed aboard the Gage for four years of conflict with the Cardassians. Following the end of the Federation-Cardassian War, Chakotay was granted an extended leave on Trebus.
In March that year, Chakotay decided to resign his commission, so upon his return to Earth he handed his resignation into Admiral Nimembeh at Starfleet Headquarters. He returned home to Trebus. (VOY episode "In the Flesh")
- Note: Since a canon source (VOY episode "In the Flesh") establishes that Chakotay left Starfleet on March 3, 2368, there's a bit of a grey zone regarding how he became involved with the Maquis. In the novel Pathways he leaves Starfleet after the Demilitarized Zone was formally established, but that did not take place until 2370. However, given the unsettled border situation (especially from a civilian standpoint, considering some settled worlds had been conceeded to the Cardassians) in the years before the formal establishment of the DMZ, it's likely the beginnings of the Maquis were forming even then. Even so, precisely what Chakotay was doing between 2368 and 2370 is still unspecified. Thus, the events of Pathways are presented below as taking place in 2370, but an altered version of them could have happened earlier than that.
In early 2370, Chakotay visited his old Academy friend Sveta on Bajor. Sveta informed Chakotay that there was a new resistance group against the Federation-Cardassian Treaty of 2370 called the Maquis. Sveta requested that Chakotay join this group and help defend his colony and others that found themselves in the Demilitarized Zone, and subject to Cardassian rule. He supported the group, but needed time to consider his options.
A few weeks later, Chakotay's life was changed forever when his village on Trebus was destroyed by a Cardassian thermalite weapon. He joined the Maquis, and was placed in command of a ship dubbed the Liberty. One of his first contacts in the Maquis is a Bajoran woman named Seska, who Chakotay became very close to. A few weeks later, Chakotay rescued B'Elanna Torres from a Bolian freighter that had been attacked by Gul Tancret and the Cardassians. After saving her, Chakotay took her to Riva Prime and Torres joined the Maquis and became the chief engineer aboard the Liberty. (VGR novel: Pathways and episode: "In the Flesh")
Around stardate 47582, Chakotay and Torres encountered the Cardassian prototype weapon, Dreadnought in the Badlands. While the self-guided weapon was meant to destroy a Maquis weapons base, Torres reprogramed the torpedo to attack a Cardassian planet. (VGR episode: "Dreadnought").
A few weeks later, the Liberty was destroyed, but all crewmembers managed to survive. Shortly after, his team managed to salvage an old fighter from a Federation surplus depot and they name the ship Geronimo. The Geronimo herself was lost in 2371, after she was destroyed by Tharia ch'Ren, a former crewmember who had seized control of the third Malkus Artifact. Thankfully, Chakotay and his crew were rescued by Cal Hudson. (VGR novella: "The Third Artifact", The Brave and the Bold, Book 2).
Following this event, Chakotay was given command of the Ju'day-class fighter Spartacus. In early 2371, the Spartacus discovered the plague-ridden planet Helena in the Demilitarized Zone. Chakotay's crew, along with Lieutenant Thomas Riker, succeeded in defeating the disease, and the mixed-race inhabitants of the planet. (TNG novel: Star Trek: Double Helix, #4: Quarantine).
A few weeks later, Chakotay assumed command of another Ju'day-class fighter, the Val Jean. He was to lead a large Maquis task force from the base on the Terikof belt to attacked the Cardassian Montee Fass shipyards in the Oliv system. However, plasma storm activity in the Badlands forced the attack to be called off, but instead they launched an attack on Opek Nor and succeeded in destoying the station.
The Val Jean was pursued by the Galor-class vessel Vetar, under the command of Gul Aman Evek, into the Badlands, where she was disabled in the plasma storms. Captain Chakotay didn't get to savour his victory, as shortly after his vessel was hit by a displacement wave created by the Caretaker, to carry them off to the Delta Quadrant. (VGR novella: Star Trek: The Badlands, Book 2; and episode: "Caretaker").
Aboard the USS Voyager
In the Delta Quadrant
Shortly after their arrival in the Delta Quadrant, Chakotay and his crew were transported to the Caretaker's Array, and examined for the viability to act as the Caretaker's successor. Three weeks later, the USS Voyager was transported to the quadrant and was similary examined. For the sake of finding a way to return to the Alpha Quadrant, Chakotay teamed up with Captain Kathryn Janeway. In the battle with the Kazon around the Array, Chakotay sacrificed the Val Jean to destroy the lead Kazon ship, and he and his crew beamed over to Voyager. When Captain Janeway decided to destroy the Array to save the Ocampa, Chakotay supported her decision and the former Maquis joined Janeway's crew with Chakotay serving as her first officer. (VGR episode: "Caretaker").
Initially, Chakotay had a difficult job of trying to merge his former crew to the crew of Voyager. In the first weeks, B'Elanna Torres and Joe Carey were competing for the chief engineer's job, which at one point came to punches. The situation was resolved and Torres became chief engineer. Several of his former crew had immense problems assimilating, and upon Chakotay's suggestion, they underwent a crash course in Academy training from Lieutenant Tuvok. (VGR episodes: "Parallax" and "Learning Curve").
After returning to Earth, Captain Janeway was promoted to the rank of Rear-Admiral(Upper). Chakotay was then promoted to the rank of Captain, and given command of Voyager. Tom Paris, who was promoted two steps in rank to Lieutenant Commander. Paris was Chakotay's first choice to become Voyager's first officer, but was overruled by Starfleet. Commander Andrew Ellis was assigned to be first officer - but Ellis was soon revealed to be a renegade changeling. After that, Lt. Commander Paris was moved up to the position of first officer. Harry Kim - who was promoted to Lieutenant - became the new chief of security after the departure of Tuvok.
In one alternate timeline where the USS Voyager was forced to turn back, Chakotay became a statesman in the Vostigye Union. He and Kathryn Janeway became lovers and would eventually have a child, Shannon Sekaya Janeway. (Star Trek: Myriad Universes novel: Places of Exile)