2000s
Hibs started the 2000-01 season with Intertoto Cup matches against Zagłębie Lubin of Poland, losing the first match 4-0 away from home and winning the return leg 1-0.
In the 2001-02 season Hibs celebrated the 80th anniversary since their foundation and the 25th anniversary since Tony Bezzina was appointed president. The club won its ninth Maltese Premier League title after a hard battle with Birkirkara FC.
Hibs kicked off season 2002-03 with matches in the UEFA Champions League First Qualifying Round against Shelbourne of Ireland. The Paolites supporters were keen to see their club play once again in this prestigious cup after 19 years. Hibs qualified for the next round after obtaining a 2-2 draw at home and a somewhat fortuitous 1-0 victory in Dublin. In the second qualifying round Hibs played against renowned Boavista of Portugal losing the first match 4-0 but drawing 3-3 at home.
In the 2003-04 season the club represented Malta in the Intertoto Cup following a fourth place finish in the previous edition of the Maltese Premier League. They were eliminated by AC Allianssi of Finland in the first qualifying round after a 1-0 defeat in Finland and a 1-1 draw at home.
In the 2004-05 season Hibs participated again in the Intertoto Cup against NK Slaven Belupo, winning the first match 2-1 in Malta but losing the return match 3-0.
Hibs opened their 2005-06 season with UEFA Cup encounters against AC Omonia Nicosia. Both matches ended in a 3-0 victory for the Cypriots. The club ended the season in good terms, winning the Maltese Cup for the seventh time after defeating Floriana 1-0 in the final.
The 2006-07 season also started with UEFA Cup ties against FC Dinamo Bucharest of Romania. The Romanians were superior and won 4-0 in Malta and 5-1 in Romania. The season ended with the eighth Maltese Cup victory for the Paolites. Hibs beat Sliema Wanderers 3-0 on penalties after the match ended in a 1-1 draw.
The 2007-08 season saw Hibs play UEFA Cup matches against FK Vojvodina Novi Sad of Serbia, losing 5-1 in Serbia and 2-0 at home. In the same season, Hibs won the Maltese Super Cup for the second time by beating Marsaxlokk 3-1. The season however proceeded badly for the Paolites as they finished in seventh place in the league, playing the last two rounds of the league in the Relegation Pool. They were also eliminated in the quarter-finals of the Maltese Cup, losing against the new league champions Valletta 2-1.
The 2008-09 season saw a massive improvement from Hibernians. In Europe they lost 3-0 on aggregate to Slovenian side ND Gorica. Under Mark Miller they managed to take the league title after a long hard battle with Valletta FC. In the last match Hibernians needed a point against Valletta FC to take the title. In a match which attracted the largest crowd for some time Hibernians kept Valletta at bay. The result ended as a stalemate (0-0) allowing Hibernians to take the title and their first star. In the FA Trophy Hibernians managed to go to the quarter finals which they lost to Sliema.
The 2009-10 season was disappointing. The lost on aggregate 6-0 to Mogren of Montenegro in the Champions League which preceded a bad season. Hibernians finished in sixth place, bottom of the Championship Pool and lost the derby against Tarxien Raindows 3 times in a row. In the FA Trophy Hiberians lost on penalties to Qormi after a 1-1 draw.
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