The rock group recently won a court ruling against the label over whether a deal signed in the pre-download age could be applied to digital sales.
"All legal disputes between the band and the company have been settled as a result of this new deal," EMI said.
An EMI statement said it would "help the band reach new and existing fans through their incredible body of work".
The band, who have sold more than 200 million albums worldwide, have been with EMI since signing their first record deal in the 1960s. The new agreement will last for five years.
They have chosen not to follow acts like The Rolling Stones, Paul McCartney, Queen and Radiohead, who have all left the label since it was taken over by private equity firm Terra Firma in 2007.
The recent court case centred around Pink Floyd's last record deal, which was signed before the days of legal downloads and said individual songs could not be sold without the band's permission.
The band argued that the rule should apply to download sales in stores such as iTunes as well as CDs, saying their "seamless" albums should not be split up.
EMI disagreed, claiming the word "record" in the band's contract applied "to the physical thing - there is nothing to suggest it applies to online distribution".
A judge sided with Pink Floyd in March, and EMI's appeal was dismissed last month.
However, single Pink Floyd tracks have remained on sale through iTunes and will continue to be available under the new deal.
Speaking in October, Pink Floyd drummer Nick Mason told BBC News it was "not actually a big punch up" with the record company, but rather "about getting a third party to adjudicate".
He also said he was "very fond" of EMI but bemoaned how "the gang known as 'business affairs' have taken over the running of the company".
"I look back with considerable fondness to the days when it was the entrepreneurs and individuals who actually ran these companies and created something that was about the music," he said.
Announcing the new deal, EMI chief executive Roger Faxon said: "Pink Floyd are one of the most important and influential bands of all time and I know I speak for everyone at EMI when I say that it is a privilege to have the opportunity to work with them."
Pink Floyd have ended a legal battle with their record company EMI and signed a new contract with the label.