In both the 2007–08 winter and 2008 summer transfer windows, Kristensen had been rumoured to be in the process of a deal with F.C. Copenhagen. On 9 July 2008 TV 2 Sporten reported that Kristensen had agreed with FCK, and only the transfer fee needed to be agreed. In the beginning, FCK and Nordsjælland could not agree on a transfer fee, so it was announced that Kristensen would join F.C. Copenhagen on 1 January 2009 on a free transfer. The clubs subsequently agreed on a transfer fee the next day, and on 15 July 2008 Kristensen became a F.C. Copenhagen player. Only two days later Kristensen played his first match for FCK. It was a UEFA Cup qualifier against Cliftonville at Mourneview Park, where he replaced William Kvist in the 69th minute. In May 2014 Thomas Kristensen secured a 3–2 Victory against Odense Boldklub in the 86th minute. This meant that FCK finished 2nd, in the league table that season.
On 27 July 2016, Kristensen was signed to A-League side Brisbane Roar. On 19 March 2017, against Adelaide United with late drama, Brisbane's goalkeeper, Michael Theo had been sent off along with Marcelo Carrusca for Adelaide. The referee had also pointed to the penalty spot. The Roar were ready to make their change. However, they used up their three substitutes, so their other goalkeeper, Jamie Young could not come on to the field. Kristensen was chosen to be their backup goalkeeper and switched jerseys from outfield to goalkeeper jersey as he faced Sergio Cirio into a penalty kick which was converted by the Adelaide striker in the 98th minute which ended into a 2–1 win for Adelaide United.
FC Helsingør
On 1 August 2019 FC Helsingør confirmed, that Kristensen had joined the club on a 1-year contract.
International career
In January 2007 Kristensen was called upon by the Danish national team, which was touring north and central America in a string of friendly games in the United States, El Salvador and Honduras, by team manager, Morten Olsen. He played the two last games of the tour against El Salvador and Honduras. In August 2007 Kristensen again was again selected by Olsen, for an A national friendly against Ireland, though he sat on the bench the whole match in the 0–4 defeat. Half a month later he was called up again for the Euro 2008 qualifiers against Sweden and Liechtenstein. Kristensen was subsequently scratched from the team due to an injury. In January 2008 Kristensen was called upon for the league national team again. This time for a tour of the Middle East. Kristensen's A national team debut came on 2008-03-26 against Czech Republic. He started the game in central midfield next to Sevilla FC player Christian Poulsen and played the first 65 minutes. In the 26th minute he made the assist to Nicklas Bendtner's goal. Kristensen was also in the squad for the friendlies against Netherlands and Poland. In these two matches he only played the last 27 minutes against Poland.
