On
August 31, 2005 Owen finally signed a four-year contract to play for Newcastle United, despite initial press speculation that he would rather have returned to Liverpool.. With the metro system being packed to the rafters with black and white shirts making their way to Central, Monument and Haymarket stations, roughly 20,000 fans were present at Newcastle's home ground of
St James' Park for Owen's official unveiling as a Newcastle player. He scored his first goal for the club on his second appearance, the second goal in a 3–0 away win at
Blackburn Rovers on
September 18 – Newcastle's first win of the season. Owen scored his first
hat-trick for Newcastle in the 4–2 away win over West Ham on
December 17. It was also a "
perfect hat trick", (A hat-trick scored with his left foot, right foot, and head).
Owen has been very unfortunate in sustaining serious injuries since joining Newcastle. On
December 31, 2005, Owen broke a
metatarsal bone in his foot in a match against
Tottenham Hotspur. He underwent
surgery to place a pin in the bone, to help speed the healing process. He was expected to be out of action until late March, but the healing process did not go as hoped and on
March 24 he underwent a second, minor, operation. Owen then stated that he should be fit for the final few weeks of the season with Newcastle. His return to action finally came against
Birmingham City on
April 29 when he came off the substitutes' bench in the 62nd minute. After the match Owen stated that he was "not 100% happy" with his foot. He underwent a further x-ray and made himself unavailable for Newcastle's final game of the season.
A damaged
anterior cruciate ligament in his right knee, sustained in the first minute of the group match against Sweden at the
2006 World Cup, kept Owen out of regular football for nearly a year, until
April 2007. Owen's injury fanned the "club or country" dispute between clubs and the international authorities, as
the Football Association's insurance policy would not fully reimburse Newcastle United for Owen's salary of over £120,000 a week, or the costs of employing another player to cover for him; Newcastle chairman Freddy Shepherd threatened to sue the FA for compensation.
Owen began light training on
12 February 2007, when pictures on the club's official website highlighted Owen running and carrying out minor exercises. He made his comeback from injury on
10 April 2007 in a 4–1 behind-closed-doors friendly against Gretna, scoring after 10 minutes and then setting up fellow striker
Shola Ameobi before coming off an hour later. Owen then started his first game for Newcastle United in over a year, against
Reading on the
30 April 2007 in a game that Newcastle United lost 1–0. He played the full 90 minutes, having a goal disallowed for
offside.
Owen was stretchered off an hour into Newcastle's game with
Watford on
13 May 2007, suffering concussion after colliding with team-mate
Matty Pattison.
On
9 May 2007, Newcastle's chairman
Freddy Shepherd reacted angrily to reports that Owen could move on to another club at the end of the
2006–07 season, due to a release clause in his contract. A report in
The Times newspaper suggested Owen could be available for less than £10m and could be a target for the likes of
Chelsea, Manchester United, Liverpool and
Arsenal. Despite these reports, Shepherd warned Owen "to show some loyalty" and warned him that "none of the big four clubs want him." However, in a video posted on
YouTube, a group of Liverpool fans asked Shepherd if they could re-sign Owen, he responded by saying that he would "carry Owen back to Liverpool" himself. Shepherd also stated his dislike of Owen's agent but praised Owen as a "good lad". This led many to believe that Owen would exercise his right to leave if the £9m valuation was matched. On
10 June 2007, Owen's new manager at Newcastle,
Sam Allardyce, confirmed the existence of the release clause in Owen's contract and admitted he feared that the club would be powerless to prevent Owen from leaving. However on
12 July 2007 Owen committed his immediate future to Newcastle United, stating: "I believe that these can be good times to be at Newcastle, which is why I am more than happy to be here."
On
17 July,2007, he scored his eighth goal for Newcastle in a pre-season friendly against Hartlepool. Several days later, Owen picked up a thigh injury in training. Newcastle manager
Sam Allardyce admitted that Owen was likely to miss the start of the forthcoming
Premier League season due to the injury which "Doesn't look as encouraging as we first thought." Owen made his comeback from injury in a club friendly on
13 August 2007 and declared himself available for Newcastle's next match, against
Aston Villa F.C., as well as England's forthcoming international matches. On
August 29 2007, Owen scored his first competitive goal for Newcastle since December 2005 when he scored in the
Carling Cup against
Barnsley. Three days later he scored in the league, with a late winner against
Wigan.
In late September 2007, after an encouraging start to the season playing for both Newcastle United and for England, it was reported that he would urgently require an operation for a double hernia and would likely be out of action for at least a month.. In his first match back from the hernia operation, he scored a late goal coming off the substitutes bench to clinch victory for Newcastle over
Everton F.C.