John Schultz’s form and Brownlow Medal win were highlights of 1960, with Footscray improving only slightly from the previous season to finish tenth. Former player Bill Findlay was appointed Whitten’s assistant coach in 1961. A meteoric rise up the ladder (due in part to a game plan centred around the ‘flick pass’ and its promotion of fast, play-on football) saw Footscray defeat Geelong in the last round to make the finals. Victory over St Kilda in the first semi-final was followed by a win against Melbourne in the preliminary final, when rover Merv Hobbs took what some consider the ‘mark of the century’ over Melbourne’s Trevor Johnson. The grand final, between Footscray and Hawthorn, was the first time two of the teams admitted to the VFL in 1925 met to play for the premiership. Footscray, led by captain/coach Ted Whitten, took an 8 point lead into the main break, but the Bulldogs wilted in the heat and Hawthorn claimed their first VFL flag, in front of 108,000 people. Footscray were well-served in the finals by Schultz, Hobbs, Bob Spargo, Alex Gardiner, Charlie Evans, Bernie Lee, John Hoiles, Bob Ware, Jack Slattery and Whitten, who won his fifth club best and fairest.

The Bulldogs made amends for 1961 by beating Hawthorn in Round 1 of 1962. Six players were chosen in the Victorian team, but Footscray could not sustain the previous year’s form, slipping to fifth – then gradually out of contention in the mid-1960s. Some players did excel: a regular Victorian representative with Whitten, John Schultz won five best and fairest awards to equal Norm Ware and Whitten; John Jillard proved a consistently capable defender; Ray Walker had a standout 1963 season; and George Bisset proved an elusive and skilful rover.

Poor on-field results and dwindling revenue resulted in changes of office in 1967. Jack Collins, secretary since 1959, took over as president. Bill Dunstan became secretary. Charlie Sutton replaced Ted Whitten as coach, but Whitten remained captain. Bert Dunne continued as treasurer, a position he had held for the whole of the decade. Despite the changes, the club finished last in 1967. In 1968, the VFL introduced country recruiting zones. Footscray were allocated Gippsland, including the Latrobe Valley and Alberton football leagues. Sutton stood down as coach for business reasons at season end and legendary ruckman John Schultz retired.

Footscray won night premierships in 1963, 1964 and 1967. This end-of-season competition was played under lights at Lakeside Oval between teams who missed the finals. At the Western Oval, the ‘cowshed’ pavilion at the Barkly Street end was pulled down in 1966 and, in 1969, a new grandstand was officially opened, named the E.J. Whitten Stand in honour of the club games record holder and coach, who reached 300 games in the first round. Fans glimpsed the future in the late 1960s when Gary Dempsey, Bernie Quinlan, Laurie Sandilands, Stephen Power and Barry Round made their respective debuts. Dempsey’s career was threatened when he was severely burned in the Truganina bushfires, forcing him to miss all but two games in 1969. George Bisset ended the decade as an unlucky runner-up in the Brownlow Medal.