On December 2, 1998, Ferentz was hired as Iowa's 26th head football coach to replace the retiring Hayden Fry.
The team struggled during Ferentz's first two seasons with a combined 4–19 record, but the Hawkeyes earned their first bowl bid of the Ferentz era after a 7–5 season in 2001.
They beat Texas Tech in the Alamo Bowl, 19–16.

The 2002 season would prove to be memorable for Ferentz and the Hawkeyes.
The team finished the regular season with an 11–1 record; its only loss coming to Iowa State.
They shared the Big Ten Conference championship with Ohio State, as both teams finished 8–0 in conference play.
Quarterback Brad Banks won the Davey O'Brien Award for best quarterback and finished second in the Heisman Trophy balloting to Carson Palmer of USC.
Tight end Dallas Clark was that season's John Mackey Award winner, and placekicker Nate Kaeding was the Lou Groza Award winner.
Ferentz was named Coach of the Year by the Associated Press for his efforts.
Iowa received its first-ever BCS invitation, losing to USC in the 2003 Orange Bowl, 38–17.

Despite losing several seniors to graduation, the Hawkeyes compiled a 9–3 regular season record in 2003.
They defeated Florida 37–17 in the Outback Bowl on January 1, 2004, for their first January win since 1959.
This earned the Hawkeyes a #8 national ranking in both the AP Poll and Coaches Poll at the end of the season.
Offensive tackle Robert Gallery was that season's Outland Trophy winner; after the season, the Oakland Raiders chose him with the second overall pick in the 2004 NFL Draft.

Ferentz had to deal with multiple injuries to the Hawkeyes' running backs and the death of his father, John, during the 2004 season.
Nevertheless, the Hawkeyes compiled a 9–2 regular season record, sharing the Big Ten Conference championship with Michigan after a 30–7 victory over Wisconsin on November 20.
 For the second time in three seasons, Ferentz was named the Big Ten Conference Coach of the Year.
On January 1, 2005, they defeated LSU, 30–25, after a thrilling 56-yard touchdown pass from Drew Tate to Warren Holloway as time expired in the Capital One Bowl.
This gave Ferentz his third straight ten-win season with the Hawkeyes and another #8 national ranking.

The Hawkeyes went 7–4 during the 2005 regular season.
After early-season losses to Iowa State and Ohio State and close losses to Michigan and Northwestern, they finished the season with wins over Wisconsin and Minnesota to earn a second trip to the Outback Bowl to face Florida on January 2, 2006.
This time, however, the Gators got a measure of revenge for their loss two years earlier, as the Hawkeyes lost to Florida, 31–24.
 Much was said about the officiating in this game, as there were 13 missed or bad calls made against the Hawkeyes that directly influenced the outcome.
 The NCAA made an official acknowledgment of this issue.

Iowa started the 2006 season strong, winning their first four games before losing to top-ranked Ohio State.
After a 5–1 start, however, the Hawkeyes collapsed down the stretch, losing five of their last six games.
Iowa suffered shocking losses to Northwestern and Indiana and lost rivalry games with Wisconsin and Minnesota.
The Hawkeyes finished the regular season with a 6–6 record and accepted an invitation to the 2006 Alamo Bowl, Iowa's sixth straight bowl game.
Playing as nine-point underdogs to defending national champions Texas, Iowa lost the Alamo Bowl by a score of 26–24.

In 2007, Ferentz' Hawkeyes started 2–4 and lost their first three conference games.
An upset victory over Illinois ended a nine-game conference losing streak for Iowa, and the Hawkeyes closed out the Big Ten season by winning their last three conference games.
 However, a disappointing loss in the season finale to Western Michigan dropped the Hawkeyes' season record to 6–6.
Though Iowa was bowl-eligible, the Hawkeyes did not receive a bowl bid, snapping Iowa's streak of six consecutive bowl appearances.

In 2008, Ferentz and the Hawkeyes started out strong with victories over his old team, Maine, Florida International, and rival Iowa State, b
On December 2, 1998, Ferentz was hired as Iowa's 26th head football coach to replace the retiring Hayden Fry. The team struggled during Ferentz's first two seasons with a combined 4–19 record, but the Hawkeyes earned their first bowl bid of the Ferentz era after a 7–5 season in 2001. They beat Texas Tech in the Alamo Bowl, 19–16.
The 2002 season would prove to be memorable for Ferentz and the Hawkeyes. The team finished the regular season with an 11–1 record; its only loss coming to Iowa State. They shared the Big Ten Conference championship with Ohio State, as both teams finished 8–0 in conference play. Quarterback Brad Banks won the Davey O'Brien Award for best quarterback and finished second in the Heisman Trophy balloting to Carson Palmer of USC. Tight end Dallas Clark was that season's John Mackey Award winner, and placekicker Nate Kaeding was the Lou Groza Award winner. Ferentz was named Coach of the Year by the Associated Press for his efforts. Iowa received its first-ever BCS invitation, losing to USC in the 2003 Orange Bowl, 38–17.
Despite losing several seniors to graduation, the Hawkeyes compiled a 9–3 regular season record in 2003. They defeated Florida 37–17 in the Outback Bowl on January 1, 2004, for their first January win since 1959. This earned the Hawkeyes a #8 national ranking in both the AP Poll and Coaches Poll at the end of the season. Offensive tackle Robert Gallery was that season's Outland Trophy winner; after the season, the Oakland Raiders chose him with the second overall pick in the 2004 NFL Draft.
Ferentz had to deal with multiple injuries to the Hawkeyes' running backs and the death of his father, John, during the 2004 season. Nevertheless, the Hawkeyes compiled a 9–2 regular season record, sharing the Big Ten Conference championship with Michigan after a 30–7 victory over Wisconsin on November 20.  For the second time in three seasons, Ferentz was named the Big Ten Conference Coach of the Year. On January 1, 2005, they defeated LSU, 30–25, after a thrilling 56-yard touchdown pass from Drew Tate to Warren Holloway as time expired in the Capital One Bowl. This gave Ferentz his third straight ten-win season with the Hawkeyes and another #8 national ranking.
The Hawkeyes went 7–4 during the 2005 regular season. After early-season losses to Iowa State and Ohio State and close losses to Michigan and Northwestern, they finished the season with wins over Wisconsin and Minnesota to earn a second trip to the Outback Bowl to face Florida on January 2, 2006. This time, however, the Gators got a measure of revenge for their loss two years earlier, as the Hawkeyes lost to Florida, 31–24.  Much was said about the officiating in this game, as there were 13 missed or bad calls made against the Hawkeyes that directly influenced the outcome.  The NCAA made an official acknowledgment of this issue.
Iowa started the 2006 season strong, winning their first four games before losing to top-ranked Ohio State. After a 5–1 start, however, the Hawkeyes collapsed down the stretch, losing five of their last six games. Iowa suffered shocking losses to Northwestern and Indiana and lost rivalry games with Wisconsin and Minnesota. The Hawkeyes finished the regular season with a 6–6 record and accepted an invitation to the 2006 Alamo Bowl, Iowa's sixth straight bowl game. Playing as nine-point underdogs to defending national champions Texas, Iowa lost the Alamo Bowl by a score of 26–24.
In 2007, Ferentz' Hawkeyes started 2–4 and lost their first three conference games. An upset victory over Illinois ended a nine-game conference losing streak for Iowa, and the Hawkeyes closed out the Big Ten season by winning their last three conference games.  However, a disappointing loss in the season finale to Western Michigan dropped the Hawkeyes' season record to 6–6. Though Iowa was bowl-eligible, the Hawkeyes did not receive a bowl bid, snapping Iowa's streak of six consecutive bowl appearances.
In 2008, Ferentz and the Hawkeyes started out strong with victories over his old team, Maine, Florida International, and rival Iowa State, b
Kirk Ferentz