Magennis began his career as an outfield player, playing up front, even representing County Down in the Milk Cup as a youngster, before eventually becoming a goalkeeper.

On 31 October 2007, Cardiff met Liverpool in the Football League Cup but, with David Forde and on-loan goalkeeper Kasper Schmeichel ineligible, Magennis took a spot on the bench for the match.

The decision to include Magennis was controversial because he had been called up to the Northern Ireland under-19 team but was not allowed to join the squad by manager Dave Jones due to the need to keep the youngster at Cardiff, with only one senior goalkeeper available for the match.

Magennis signed his first professional contract on 10 April 2009 for Cardiff City,[5] the only second year academy student to be offered a professional deal, and began working with reserve team coach Paul Wilkinson who had previously coached former Cardiff striker Cameron Jerome in a similar manner.

On 8 August 2009, Magennis made his professional debut when he replaced Jay Bothroyd as a late substitute on the opening day of the 2009–10 season in a 4–0 win over Scunthorpe United.

[6] In his fourth appearance for the club, Magennis scored his first professional goal during a 3–1 win over Bristol Rovers in the second round of the League Cup.

[7] The return of Ross McCormack and Warren Feeney from injury meant that Magennis fell down the pecking order at Cardiff and he was allowed to join League Two side Grimsby Town on a one-month loan deal on 15 October 2009[8] He made his debut against Rochdale on 17 October 2009, which was to be the last game managed by Mike Newell, who was sacked the following morning.

Magennis made just one more appearance for the side before, on 29 October 2009, he was told that he and fellow loanee Arnaud Mendys loan contracts were to be terminated ahead of schedule.

"[9] Magennis made his first start for Cardiff on 9 January 2010 in a 1–1 draw with Blackpool,[10] but was forced off after just 35 minutes after suffering a fractured fibula.

He was given a free transfer by Cardiff at the end of the season along with Peter Enckelman, Warren Feeney, Tony Capaldi and Aaron Morris.

[15] He started in Aberdeen's first game of the 2010–11 season at home to Hamilton Academical, where he hit the crossbar in a 4–0 win and played 90 minutes.

In the pre-season friendly against German side Borussia Mönchengladbach, which Aberdeen lost 5–2, Magennis scored from 45 yards.

[26] Soon after scoring his first goal of the season, Manager Craig Brown began negotiating with Magennis to sign a new contract.

Earlier that day he had been left out of Kilmarnock's squad to play Motherwell, with manager Lee Clark saying Magennis had told him he "didn't feel right for today's game.

[55] Magennis made his first appearance for Hull City in the first round of the EFL Cup in the 0–3 away win against Tranmere Rovers.

In July 2009, Magennis helped Northern Ireland retain their Milk Cup crown, scoring the first goal in their 2–0 final victory against Denmark.

As a teenager, Magennis revealed he once nearly quit football for rugby after struggling as a goalkeeper before eventually switching position to striker.