The team, which trains every week on a set of artifical pitches in Mereway, won the Stephen Thomas tournament in Cirencester over the weekend.
A spokesman for the Cobblers said the club thanked hosts Swindon Town for their hospitality before congratulating the Downs' syndrome squad on their title.
He added: "Well done Richard (coach) and the rest of the squad - everyone at Northampton Town Football Club is very proud of you."
The team trains at the Goals Centre in Northampton every Sunday from 10.30am until noon and are on the look out for new members as they look to play more matches against other Downs' syndrome teams across the country.
In recent years the squad has played against other Down's syndrome teams including Swindon Town, Lincoln City, Coventry City and Norwich City, as well as competing in the National Finals of the Downs' syndrome Cup.
Anyone wanting more details about the squad and training should email Russell Lewis: russell.lewis@ntfc.co.uk