As the team prepared for its inaugural season, Bill Becher was named the first head coach of the club and forward David Bascome was signed as the first player.

The City Islanders won their first match 5–2 on the road against the Northern Virginia Royals with Steve Fisher scoring the club's first ever goal.

On March 1, 2010, the City Islanders entered into an agreement to become the official USL affiliate of Major League Soccer's Philadelphia Union.

The affiliation would soon have City Islanders defender, Sheanon Williams sign with the Union and become an immediate insertion in the first tier club's starting eleven.

[8] Shortly before the 2017 season, George Altirs was announced as new majority owner of the club so as to "stay in Harrisburg and build an international developmental base that is unique and exciting."

As majority owner, Altirs "will oversee the technical side of the club, including player and staff selections, transfers, and outside, non-local partnerships for the Harrisburg City Islanders."

[10] Ahead of the 2018 season, Penn FC made some key signings including the return of former City Islander standouts Ken Tribbett and Lucky Mkosana, and forward Tommy Heinemann.

Conflicts with baseball operations and schedule at FNB Field required the team to have long away stints until a final 9-match home stand.

[16] In December 2019, during the USL Winter Meetings, reports noted that the club had ceased operations and no longer had any employees on payroll after 16 years of professional soccer.

[4] Penn FC also competes in the U.S. Open Cup, where they developed a reputation as "giant killers" for defeating several teams from Major League Soccer.

The City Islanders first competed in the U.S. Open Cup in 2007, defeating two amateur squads before upsetting D.C. United 1–0 to reach the quarterfinals.

The City Islanders repeated the feat in 2010, knocking off Major League Soccer's New York Red Bulls 1–0 in the round of 16 and claiming a cash prize for advancing furthest of any USL Pro team in the tournament.

The City Islanders again dispatched the New England Revolution in the 2012 edition of the U.S. Open Cup, prevailing on penalty kicks after a 3–3 draw in the round of 32.

The following year's matchup was staged at Cumberland Valley High School, where 5,133 fans turned out to witness Freddy Adu and United prevail 2–1.

On March 1, 2010, the City Islanders entered into an agreement to become the official USL affiliate of Major League Soccer's Philadelphia Union.

As part of their affiliation, the City Islanders host annual friendly matches against the Philadelphia Union of Major League Soccer.

[17] The City Islanders carried a 2–0 lead into halftime behind goals by Nelson Becerra and Andrew Welker, but heavy substitutions allowed the Union to demonstrate their superior depth, and they scored five times in thirty minutes before Jose Angulo pegged one back.

Jorge Perlaza and Kai Herdling scored for the Union, while a brace by Garret Pettis and goal by Yann Ekra carried the USL-PRO outfit to the 3–2 victory.

[18] After five years of cooperation, it was announced on August 19, 2015 that the affiliation would dissolve at the conclusion of the 2015 season as the Union would develop their own USL team, Bethlehem Steel FC, in the Lehigh Valley starting in 2016.

[20][21] In 2016, the City Islanders alternatively dropped "Harrisburg" from the team's title in an attempt to increase the club's footprint in central Pennsylvania.

The City Islanders also compete at Clipper Magazine Stadium in Lancaster, Pennsylvania which serves as an alternate home ground during the 2016 season.

[24] This expansion is intended to meet the minimum capacity required by the USSF for a league to compete as Division 2 in the American soccer pyramid.

[30] The goal of the partnership was to provide the academy with a professional team to be at the pinnacle of the Rush Soccer development program, drawing from large player pools and international affiliations.

Home match broadcasting is provided live by Inivca where play-by-play announcing covered by Brian Keyser with color commentary by Charlie Gerow.

[5] Although they had been rivals and competed against each other in previous seasons, the inaugural Keystone Derby was officially contested between Penn FC and the Pittsburgh Riverhounds in 2015.