Kranjčar made his Premier League debut for Portsmouth on 1 October 2006 as he played all 90 minutes in their 2–1 away defeat to Tottenham Hotspur.
He scored his first Premier League goal on 31 March 2007 at Fulham, giving Portsmouth an early 1–0 lead in a match that eventually ended in a 1–1 draw.
He made a total of 24 appearances and scored two goals in his first Premier League season.
The following season, he played an integral role in Portsmouth's FA Cup win.

At the beginning of the 2008–09 season, AS Monaco apparently had a bid of £12 million rejected for Kranjčar, however this was denied by Monaco.
On 12 February 2009, with Portsmouth battling relegation, Kranjčar publicly declared his desire to quit Portsmouth and move to a bigger club.
Arsenal and AS Monaco have previously been linked with moves for the Croatian International.
Everton manager David Moyes also expressed an interest in signing Kranjčar as a replacement for long-term absentee Mikel Arteta.
In August, Kranjčar stated: "For now I am staying, but we have not strengthened like I would have liked us to.
That's why I will not sign a new contract.
It's one more season for me and then I'm off".
Kranjčar made his Premier League debut for Portsmouth on 1 October 2006 as he played all 90 minutes in their 2–1 away defeat to Tottenham Hotspur. He scored his first Premier League goal on 31 March 2007 at Fulham, giving Portsmouth an early 1–0 lead in a match that eventually ended in a 1–1 draw. He made a total of 24 appearances and scored two goals in his first Premier League season. The following season, he played an integral role in Portsmouth's FA Cup win.
At the beginning of the 2008–09 season, AS Monaco apparently had a bid of £12 million rejected for Kranjčar, however this was denied by Monaco. On 12 February 2009, with Portsmouth battling relegation, Kranjčar publicly declared his desire to quit Portsmouth and move to a bigger club. Arsenal and AS Monaco have previously been linked with moves for the Croatian International. Everton manager David Moyes also expressed an interest in signing Kranjčar as a replacement for long-term absentee Mikel Arteta. In August, Kranjčar stated: "For now I am staying, but we have not strengthened like I would have liked us to. That's why I will not sign a new contract. It's one more season for me and then I'm off".
Niko Kranjčar