More than 150 teams took part in the tournament, which this year was hosted by Farnham, Cranleigh and Farncombe.
Farnham’s under-12 side, two under-13 teams, the under-15s and under-17s all won their individual tournaments to help the club top the table.
A club spokesman said: “It was a fantastic achievement from everyone involved and shows the massive progress of Farnham United over the past two seasons, going from six teams then to now nearly 400 youngsters across nearly 40 teams – and winning the Waverley Cup!
“These are exciting times for the club, particularly with the forthcoming merger with Farnham Town.
“We will be forming a new Farnham Town Youth Club, with nearly 70 teams representing the club and the town across the Surrey and Hampshire leagues.”
At under-13 level, Farnham United had a phenomenal season.
The under-13 Panthers won the North East Hants Youth League Premier division and the under-13 Hawks clinched the Surrey Primary Premier Elite division.
The under-13 Lions finished fourth in the Surrey Primary Premier Elite division while the under-13 Hawks beat the Aldershot & District Schools representative team and recently won the Aldershot boys’ and girls’ tournaments.
The club spokesman added: “Next season will see this age group test themselves in the Junior Premier League on Saturdays, competing with the likes of Woking, Bracknell, Oxford, Bromley and so on, while also moving to the Surrey Youth League on Sundays, to test themselves against the best teams from all across Surrey.
“We’re excited to take this next step with the group and would be keen to hear from any local players who would like to come and test themselves against the best next season.”