The harbour finished second to Port Everglades in Miami, with Port Toulon in France finishing third.
Winners were announced at the Seatrade Europe Exhibition in Hamburg.
Councillor James Stockan, chair of the council’s infrastructure and development committee, said: “This is an exceptional achievement for a small port - to have been considered alongside massive destination ports for such a prestigious award and to be runner up.
“This is a worldwide award and we were the only UK Port in the final short list.
“I’d like to applaud the work of the Council’s team and all the partners and tourism operators involved who make sure Orkney and Kirkwall puts on such a good welcome for every cruise liner.”
Michael Morrison, business development manager for Orkney Islands Council’s marine services, who was at the awards ceremony, said he would be proudly displaying the award certificate on the Cruise Scotland stand at the Seatrade Exhibition this week.
He added: “To come runner up in a global award at this level is brilliant – and is testimony to the passion and commitment of the team who deliver cruise ship services in Orkney.
“The feedback from cruise lines is that the customer service ratings or port calls into Orkney are better than for any other UK port. That is something we must strive to maintain and improve in the years ahead.”
The Port of the Year category is specified as ‘a port authority/port management company which has made significant improvements to its handling facilities/ cruise – tourism infrastructure over the past 12 months.
The award is judged by a panel of 16 from throughout the industry world-wide.
Orkney received 73 visits by cruise ships carrying around 60,000 passengers in 2013.
Another 73 visits are already booked for next year by liners which will bring around 64,000 passengers to Orkney.
Fifteen liners have already booked for 2015, and there are already some bookings for 2016.