Fowler's season picked up from there as he scored several important goals including one against runaway champions Manchester United and a free kick in the FA Cup semi-final against Wycombe Wanderers. Fowler featured as a substitute in the 2001 FA Cup Final coming on as a 77th-minute replacement for Vladimír Šmicer. Liverpool, who were 1–0 down at that point, eventually won the game 2–1 with two goals from Owen. Fowler raised the trophy along with Sami Hyypiä and Jamie Redknapp.
Fowler began the 2001–02 season controversially, after being dropped by the then manager Gérard Houllier from the Liverpool squad for the 2001 Charity Shield match, following a training ground confrontation with assistant manager Phil Thompson. He made an appearance in Liverpool's 3–2 European Super Cup victory over Bayern Munich, but starts were intermittent. In October 2001, he scored his first league hat-trick for three years, helping Liverpool beat Leicester City 4–1, but was dropped for the following league match. Though Fowler had been on a contract extension from 1999 (unlike Steve McManaman – who exercised his Bosman entitlement the very same year), Fowler was linked to Lazio, Arsenal and Leeds United, and Liverpool's management as well as fans and the media constantly reported that what happened with McManaman (regarded as a huge financial loss) would never be repeated and thus the club never rejected those bids without consideration. This meant that coupled with Fowler's relationship with Houllier, speculation over Fowler's future persisted for most of Houllier's tenure and became an issue that divided Liverpool fans. His last appearance for Liverpool was against Sunderland, in which he was substituted at half-time.
The transfer went ahead just one month after his hat-trick at Leicester. He made his Leeds debut in an away game against Fulham in December 2001, the same ground where he had made his Liverpool debut eight years earlier. Fowler scored 12 goals in the remainder of the season, helping Leeds to a UEFA Cup qualifying place. Fowler was included in the England squad for the 2002 World Cup, but only made one appearance, coming on as a substitute in a second-round win over Denmark.
Fowler scored his fourth goal for England on 25 May 2001, netting the second goal in the 4–0 friendly win against Mexico at Pride Park, Derby. On 5 September, he scored his first competitive goal for England in the 2–0 win against Albania at St James' Park, Newcastle. This was during qualifying for the 2002 FIFA World Cup. England qualified for the World Cup, and after scoring in friendlies against Italy and Cameroon, Fowler was selected in Sven-Göran Eriksson's 23-man squad for the tournament in South Korea and Japan. He didn't appear in any of England's group matches, but on 15 June 2002, he came on as a second-half substitute in the 3–0 win against Denmark in the Round of 16. This turned out to be Fowler's last cap for his country. He won a total of 26 caps for England and scored 7 goals.
Fowler married wife Kerrie on 9 June 2001 in the town of Duns, Scottish Borders in Scotland. Together they have three daughters and one son.