The team's first season was a winning one, as they took the Great Lakes Division with a 15–1–4 record, ten points clear of second place West Michigan Edge, and into the playoffs at the first time of asking.

Their opponent in the semi-final was Mid-South Division champs Texas Spurs who they beat 1–0; unfortunately for the Fire, they lost the Central Conference championship game to Heartland Division champions Sioux Falls Spitfire (who went on to finish third in the national playoffs), but is still marked an excellent debut for the team – so much so that head coach Bret Hall was named PDL Coach of the Year in the end of season awards.

Despite this unexpected loss, Chicago remained a force to be reckoned with in the Central Conference, as evidenced by the fact that goalkeeper Matt Pickens and defender Denny Clanton were named the 'Best of the Year' for their respective positions by the PDL.

Chicago's 2003 campaign was the most successful in their history to date; despite losing their opening salvo 2–0 away at Des Moines Menace, the Fire recovered to rattle off eight consecutive wins in their next eight games, including a 5–0 drubbing of Sioux Falls Spitfire that featured a Robert Mouw hat trick, three 4-goal victories over St. Louis, Thunder Bay and Kansas, and a four-game streak in mid June where they did not concede a single goal.

The playoffs were hosted by the Michigan Bucks, and Fire progressed in impressive form with an 8–0 demolition of Indiana Invaders in the semi-final that saw Patrick Grange, Jamal Sutton and Kirk Harwat each grab two goals each.

Fire's fairytale run ended in the third round with a 1–0 defeat at the hands of A-League side Rochester Raging Rhinos, but their efforts still illustrated the strength of the team.

The 2004 Fire team was awash with future stars: in addition to top scorers Nowaf Jaman and Julian Nash, who scored 12 goals each, players such as Drew Moor, Dasan Robinson, Chris Rolfe all featured for the team, while goalkeeper Brad Guzan posted the best GK stats in the PDL – 0.388 goals against – before turning pro with Chivas USA.

Fire moved back to the Great Lakes division in 2005, but still ran away with their fifth divisional title in five years, enjoying a superb 14–1–1 record, nine points clear of second-placed Michigan Bucks.

The team changed its name to Chicago Fire Premier in 2006, and made it six for six in league play, taking Great Lakes Division once more with an impressive 14–2–0 regular season record, 12 points clear of perennial bridesmaids, Michigan Bucks.

Striker Ryan Anderson scored a hat trick in the 4–0 win over Indiana Invaders in late May, and then held on to take a 4–3 victory in the see-sawing return fixture in South Bend in June.

Fire's biggest win of the season was the 5–0 hammering of Fort Wayne Fever in mid-June that featured a brace from substitute striker Strider Elass, but they were already too far behind Michigan to catch them on the run-in, and were lucky not to be caught at the post themselves with two more losses in July, including a 2–0 final day defeat to Cleveland.

Fire started the 2009 season superbly, winning four of their first five games, including three back-to-back road victories over Cleveland, Fort Wayne and Toronto, and qualifying for the U.S. Open Cup.

Their cup run was brief but satisfying, beating the National Premier Soccer League's Milwaukee Bavarians before falling to the professional Minnesota Thunder 4–0 in the second round.

Elsewhere, however, Chicago were virtually flawless; they outclassed the Michigan Bucks 3–0 in early July, put five past the Cincinnati Kings, and ended Forest City London's hopes of a divisional title with a 3–1 win in mid-July.

Subsequent victories over Kalamazoo and the Ocean City Barons gave Chicago a second Conference title; they overcame the Cary Clarets 2–1 in extra time in a bad-tempered semi-final in which two players and two coaches were red carded, and travelled to California for the PDL Championship game against Ventura County Fusion.

Despite having a numerical advantage for more than an hour, Chicago were beaten by an injury time goal from Ventura's Alfonso Motagalvan, and had to be content with the runners up spot.