The premises in Fernwood Road, Jesmond, were raided overnight on April 1-2 and also among the haul - valued at around £150,000 - were a lock of hair from Admiral Lord Collingwood and a large amount of antique silverware.
Newcastle Temporary Superintendent Bruce Storey said: "The Nobel Peace Prize dates back to 1934 when it was awarded to Henderson for his work on international disarmament. The prize has been awarded 93 times to 124 Nobel Laureates between 1901 and 2012 and so the stolen item is extremely rare, recognisable and historically important."
This is believed to be the first theft of a Nobel Peace Prize.
Henderson (1863-1935) was the Labour Party's first ever Cabinet minister. In 1900 he attended the London conference which set up the Labour Representation Committee and was elected to parliament in 1903, before chairing the conference in 1906 which formed the Labour Party (he was secretary from 1911-34). He had a remarkable record of winning five times and losing five times in general elections, but regaining a seat after each of the losses by winning by-elections.
He was a leading figure in the League of Nations' disarmament effort - which ultimately failed as the world hurtled towards the Second World War.
Henderson was born in Glasgow but moved to Newcastle aged nine. The medal was presented to the city council about 25 years after his death. A rose bowl presented to him when he was given the freedom of the city in 1930 was also stolen. Admiral Lord Collingwood, Nelson's second-in-command at Trafalgar, was another notable figure with strong connections to the North East, and was in fact born in Newcastle in 1748.
Anyone with information should contact police on the 101 non-emergency number or call Crimestoppers on 0800 555111.
