1996 – Beginning of internet connectivity at the school
1998 – The Primary School quadrangle opens
1999 – Captain Matthew Flinders Bicentenary (1799-1999) is celebrated.
1999 – The College celebrates 10 years of foundation!
1999 – Principal Stephen Matthew retires (1989-1999). Anthony Vincent commences as Principal (1999-2013)
1999 – Bruce Winther commences as Head of Primary
1999 – Inaugural cricket Firsts Versus Old Flinderians match is held.
2000 – College Production – “This is where we came in”
2000 – Erol the Emu is adopted at three weeks old. Errol is still living his best life at the Flinders Farm.
2000 – Masterplan commences to build Design Technology and Secondary Library, upper floor Music and Drama block, and a new Primary Administration building.
2000 – Chairman John Stevenson retires. Stephen Philips commences as Chairman of the Flinders Board.