In 1997, Yarraville again took top spot and again took on Parkside in the Grand Final, but this time were able to win the flag.

In 1998, Yarraville suffered after losing many of the players who had helped win the flags the previous year and would finish midway through the ladder.

From 2001 to 2006 Yarraville maintained its spot in 1st division and just missed out on playing finals several times.

During the 2006 season Yarraville began talks about a possible merger with the Seddon Football Club.

Seddon had dropped out of the senior competition after 10 games due to poor performance.

The Yarraville Football Club played its final game at the end of the 2006 season when they defeated St Albans.