In 2001 the Club's President attended the Melbourne City Council Royal Park Master Plan meetings to keep alive the possibility of redesigning the course with new clubrooms and a bridge over the railway line on the agenda. The committee aimed to achieve a contiguous course for its members and public alike.

During 2002 Melbourne City Council renovated the pro-shop and clubhouse, added a veranda to the structure and repainted the building. The size of the clubrooms was reduced, and the pot belly stove installed by the Club in 1991 was replaced with modern gas heaters.

By 2003 the Club's membership was 74 full members, including five women and 10 juniors. Membership fees were $60 for full members and $30 for juniors. Green fees were $15.40 for 18 holes and $9.40 for 9 holes.

The Club celebrated its centenary year with a Centenary Weekend of Golf on 29 and 30 March. The Lord Mayor attended on the Saturday night to present prizes for the Saturday tournament, and Peter Thomson attended on Sunday afternoon to present prizes for the Sunday tournaments.

The Junior Pennant team won its third VGL Pennant Premiership in a row, the 2003 year in Division 1 and the two previous years in Division 2. The Scratch team won their Division 6 Pennant final, making it a very successful year for the Club during the 2003 season.

In 2004 the Club won the VGL Pennant (Handicap) Premiership, recruited more Juniors for their pennant side and a few more female members for the 9 hole competitions.

By 2006 the Club was unable to field a Junior Pennant side, and withdrew from that year's VGL competition, with much dismay. They decided to put the money saved by withdrawing from the competition towards Junior Development and it paid off. By the end of 2006 there were 10 new junior members, aged between 10 and 16 and 2007 looks like a good year for Junior Pennant. The Club also only fielded one senior Pennant side (handicap) and were defeated narrowly to Forest Hills in the VGL Finals at Werribee Park.

In March 2007 the Club hosted a "Return to Royal Park" match for a group of ex-members who were members in the 1950s. Most of the players were in the 1954 "Invincibles" team, winning the title without losing a single match in any of the five rounds

During 2009 Melbourne City Council again renovated the pro-shop and clubhouse area, swapping the proshop area with the area occupied by all Clubs who use the course. The size of the clubroom was more than halved, and the use of a kitchen and bar area were lost. Despite the upheavals during this period, the Club won its Division 8 Handicap final against Altona Lakes 5-2 .

The Club hosted the 4th annual Return to Royal Park event on March 8th 2010, which had been renamed the Tony Thomson Memorial Return to Royal Park competition in 2009. The 2010 winner was Tony's son David, who had played in the event since 2008.