He worked extensively with All-American running back Greg Hill, who was selected by the Kansas City Chiefs in the first round of the 1994 NFL draft.

[20] Kubiak was named the second head coach in Houston Texans history on January 26, 2006, replacing the fired Dom Capers.

However, Kubiak's promising campaign quickly turned disastrous as the Texans lost eight of their final 10 games, placing them third in the AFC South, with a record of 6–10.

Despite debilitating injuries to elite players including wide receiver Andre Johnson and NFL top running back Arian Foster, as well as the devastating November 13, 2011, loss of quarterback Matt Schaub, who was having a solid year, for the season, the Texans secured their first AFC South Championship and first appearance in the NFL playoffs.

[33] The Texans, with rookie fifth-round selection T. J. Yates at quarterback, defeated the Cincinnati Bengals by a score of 31–10 on January 7, 2012, in the first playoff game in franchise history, with a record crowd of 71,725 at Reliant Stadium.

[39] An NFL report on Monday, November 4, 2013, indicated that he had suffered a transient ischemic attack (TIA), or relatively brief, non-permanent symptoms of disorientation, confusion, dizziness, forgetfulness, and/or vertigo (among many other possibilities), that occurs when a blood vessel or vessels in part(s) of the brain are temporarily but not permanently blocked, usually by a stationary clot (a thrombus) or one that has broken off and traveled to occlude another area (an embolus).

[40][41] In Kubiak's absence for the second half between the Colts, defensive coordinator Wade Phillips assumed the head-coaching duties and was the acting head coach for the remainder of the game.

[44] He served one season under John Harbaugh, replacing Jim Caldwell, who signed as the head coach of the Detroit Lions in the offseason.

[45] Prior to Kubiak's hiring by the Ravens, he interviewed for the vacant head coaching spot for the Detroit Lions, which would be taken by Caldwell on January 14, 2014.

[48] Under his guidance, the Ravens had their most successful offense in 19 years, with quarterback Joe Flacco and running back Justin Forsett achieving career single-season highs in yards and touchdowns.

In addition, the 39-year-old Manning had his worst statistical season since his rookie year due to plantar fasciitis in his heel that he had suffered since the summer.

He set the NFL's all-time record for career passing yards in this game, but after throwing four interceptions, Kubiak benched Manning in the third quarter of the 29–13 home loss to the Kansas City Chiefs, in favor of backup quarterback Brock Osweiler, who took over as the starter for most of the remainder of the regular season.

During the Week 17 regular season finale, however, where the Broncos were losing by a score of 13–7 against the 4–11 San Diego Chargers, Kubiak benched Osweiler and Manning re-claimed the starting quarterback position for the playoffs by leading the team to a key 27–20 win that enabled the team to finish the 2015 regular season with a 12–4 record, winning the AFC West and securing the number-one playoff seed in the AFC.

[55][56] In the postseason, the Broncos defeated the Pittsburgh Steelers by a score of 23–16 in the divisional round and the New England Patriots 20–18 in the AFC Championship game, advancing to Super Bowl 50.

Additionally, shortly after the Broncos' Week 5 loss to the Atlanta Falcons, Kubiak was rushed to a Denver-area hospital after experiencing flu-like symptoms and extreme body fatigue.

[60] Kubiak led the Broncos to another winning season, but despite the 9–7 record, the team missed the playoffs for the first time after five straight division championships.

Following a 24–6 victory over the Oakland Raiders in the regular season finale on January 1, 2017, Kubiak announced in a meeting with his team that he was stepping down from his position due to health issues.

[61][62] He made his retirement official during a press conference the next day, calling it an "extremely difficult decision" and thanking Elway, CEO Joe Ellis, owner Pat Bowlen, and the Broncos fans for their support of him.

[67][68] However, the Broncos would reverse that decision days later due to disagreements with newly appointed head coach Vic Fangio on the team's potential offensive philosophy and staffing.

[69] While he had the opportunity to remain on the personnel department, Kubiak decided to leave the organization after spending a total of nearly a quarter century with the Denver Broncos.

[70] Kubiak also interviewed for the Jacksonville Jaguars' vacant offensive coordinator spot in early 2019, a job that eventually went to John DeFilippo.

[72] He was promoted to offensive coordinator in 2020 following the departure of Kevin Stefanski, who left to accept the head coaching position of the Cleveland Browns.

[77] Basing himself out of his home in Texas, Kubiak would analyze offensive college prospects ahead of the draft and assist in free agency.