Believing that his football career was over after the NAIA championship, Kitna finished his math education degree at Central Washington and began applying for high-school coaching jobs.
On December 14, he had his first career start against the Oakland Raiders after Moon injured his ribs, leading the team to the second biggest comeback in franchise history, from a 21–3 halftime deficit to a 22–21 win.
He made the first start of the season and second of his career against the Tennessee Oilers and earned AFC Offensive Player of the Week honors, after passing for 298 yards, 2 touchdowns and one interception, while leading a fourth-quarter comeback for the deciding 48-yard field goal in a 20–18 win.
In the fifteenth game against the Indianapolis Colts, he rallied the team to score 17 fourth quarter points in a 27–23 win, making 16-of-29 completions for 177 yards, 1 touchdown and no interceptions.
He did not play in the second game against the Chicago Bears due to a sprained toe he suffered in the season opener against the Detroit Lions.
In 2000, Seahawks head coach Mike Holmgren was concerned with Kitna's preseason performance and tried to work a trade for Green Bay Packers backup quarterback Matt Hasselbeck, although it did not come through.
[4] Kitna began the season with a four-interception performance against the Miami Dolphins, which opened the door for Holmgren to put second-year quarterback Brock Huard in the game.
On November 5, down 15–14 on 3rd-and-16 with 1:28 left in the game, Kitna dodged a possible 17-yard sack by San Diego Chargers defensive end Neil Smith and made an 18-yard pass to Darrell Jackson.
His last win for the Seahawks came on a rain-soaked Husky Stadium turf in December of that year, beating the AFC Championship Game-bound Oakland Raiders on a touchdown pass to rookie Darrell Jackson in the final minute of play.
In the sixteenth game overtime 26–23 win against the Pittsburgh Steelers, he threw for a franchise-record 68 passes, tied for the third most in NFL history.
In the fifteenth game against the New Orleans Saints, he led the offense on a pair of fourth-quarter touchdown drives to overcome a 7–13 deficit and get a 20–13 win.
In the thirteenth game against the Pittsburgh Steelers, he led a 24–20 comeback win, making a game-winning 18-yard touchdown pass with 13 seconds remaining.
He was named the NFL Comeback Player of the Year after throwing for over 3,500 yards and 26 touchdown passes (second in the AFC) in leading the Bengals to an 8–8 record, the team's first non-losing season since 1996.
Kitna was the backup quarterback until seeing his first action of the season in the thirteenth game against the New England Patriots, due to a season-ending knee injury to Palmer.
Kitna entered his first game of the season during the fourth quarter against the Detroit Lions and led the offense on a field goal drive.
He replaced Palmer in the second quarter of the season finale against the Kansas City Chiefs, completing 13-of-24 passes for 76 yards and 2 interceptions in a 37–3 loss.
He was unexpectedly thrust back behind center during the Bengals' AFC Wild Card Playoff game against the Pittsburgh Steelers on January 8, 2006.
Palmer went down with a left knee injury on his second play from scrimmage and Kitna stepped in off the bench and into a relief role.
Kitna finished 24-of-40 for 197 yards, one touchdown and 2 interceptions and one fumble as the Bengals fell to the eventual Super Bowl XL champion Pittsburgh Steelers 31–17.
The Lions offense was ranked ninth in the league in passing, with Kitna starting all 16 games, while throwing for 4,068 yards, 18 touchdowns and 20 interceptions.
Kitna suffered a back injury in the fourth game of the season and was placed on the injured reserve list on October 14.
In 2009, the Cowboys acquired Kitna to improve their backup quarterback situation, after Brad Johnson had a 1–2 record, including a 35–14 loss against the New York Giants when Tony Romo was injured during the previous season.
In 2010, Kitna remained idle until October 25, when Romo suffered a broken clavicle against the New York Giants and was later placed on the injured reserve list on December 21.
[12] Kitna ended up suffering an abdominal injury against the Arizona Cardinals on Christmas Day, and was replaced with second-year quarterback Stephen McGee for the rest of the season.
Kitna played well in relief of Romo throwing for 2,365 yards, 16 touchdowns and 12 interceptions in the 9 games he started, compiling a 4–5 record and a career-high 88.9 passer rating in the process.
[14] On Christmas Eve, 2013, Kitna was called out of retirement to serve as an emergency back-up behind quarterback Kyle Orton, for the season finale against the Philadelphia Eagles, following a back injury to Romo.
[18][19] Lincoln shared the Washington Interscholastic Activities Association (WIAA) District 3A Narrows regular season championship in 2013, with a 5–1 conference record tied with Lacey Timberline.
In February 2023, Kitna was hired as the head football coach and dean of students at Lakota East High School in Liberty Township, Ohio.