Underlying earnings per share were 9.3 pence, compared to 8.1 pence a year ago.
"After four consecutive years of profit growth, margins in our United Kingdom business declined due to a more competitive market environment, especially for holidays to Spain", Fankhauser said.
Thomas Cook Group PLC's (LON:TCG) said a successful turnaround of its German airline Condor helped the group to deliver full year profit and revenue growth.
Earnings at its United Kingdom division fell by 40 per cent in the year to September 30th, standing at £52 million.
"Momentum in Condor and Continental Europe is encouraging, but United Kingdom profits and margins are down and commentary is more cautious than we would like to see given the challenging macro backdrop", analysts at Panmure Gordon said in a note.
It said current trading was in line with expectations - with bookings up 1% in the United Kingdom - led by a return in demand for winter breaks in Egypt and the Canaries.
Chief executive Peter Fankhauser said that the performance of Condor, which improved profits by 24 million pounds in the year, was a highlight for the group's airline business, and was especially encouraging in a year when carriers Air Berlin, Monarch and Alitalia have all gone into administration.
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Group revenue rose nine per cent on a like-for-like basis to £9bn, with underlying earnings before interest and tax rising £24m to £330m.
The company said trading for the winter season was meeting expectations, with bookings up 5% thanks to steady demand for trips to the Canaries and a "strong recovery" in holidays to Egypt.
Egypt and Tunisia have suffered terror attacks while political turmoil in Turkey has also affected its sizeable tourism industry.
"Demand for our holidays to Turkey and Egypt is very strong, which we expect will start to alleviate the margin pressures caused by the high concentration of holidays to Spain in 2016 and 2017", the company said.
"I'm particularly pleased by the number of new customers we've won this year, showing us that we're getting more people to look again at what we offer - and that more of our existing customers are recommending our holidays to family and friends".
Fankhauser said recent deals with Expedia and LMEY Investments will strengthen its hotel offering.
Fiona Cincotta, a senior market analyst at City Index, said while Thomas Cook's group-wide revenues were ahead of market expectations, investors were focusing on the hit to profit margins.