The team plays its home games at the Skyline Sports Complex, located on Harrisburg's City Island, where they have played since 2004. The team's colors are tropical blue, navy blue, and white. Their current head coach is Bill Becher.
The City Islanders were powerful contenders in the second division, finishing fifth in their inaugural season and qualifying for the playoffs, where they were eliminated in the first round by the Pittsburgh Riverhounds. The City Islanders improved on this showing in their second year, as they finished third in the league with a 12–3–5 record, but were eliminated from the playoffs by the eventual champions, the Charlotte Eagles. In 2005, Bill Becher was named USL-2 Coach of the Year, while Chad Severs was named Rookie of the Year before moving on to the Rochester Raging Rhinos. In 2006, the club failed to reach the playoffs, but in 2007, the Islanders won the USL Second Division Championship, defeating the Richmond Kickers on penalty kicks. The City Islanders qualified for the playoffs in 2008 and 2009 but were unable to duplicate their championship form. Danny Cepero played for Harrisburg on loan from the New York Red Bulls in 2008, and upon returning to New York, became the first goalkeeper in Major League Soccer history to score from open play. In 2009, Ty Shipalane became the second City Islander to win Rookie of the Year and became the first City Islander to jump directly to Major League Soccer after signing with D.C. United at the conclusion of the season. After missing the playoffs for just the second time in franchise history in 2010, Harrisburg won the USL Pro National Division title to again advance to the USL Pro final, falling to the regular-season champion Orlando City Soccer Club on penalty kicks.
The City Islanders also compete in the Lamar Hunt U.S. Open Cup, where they developed a reputation as "giant killers" for defeating several teams from Major League Soccer. Harrisburg boasts an overall record of 12–5–3 in the competition, including a perfect 5–0 mark against teams from the Premier Development League and 4–4-1 record against MLS clubs. The City Islanders first competed in the Lamar Hunt U.S. Open Cup in 2007, defeating two amateur squads before upsetting D.C. United 1–0 to reach the quarterfinals. They subsequently lost to the New England Revolution 1–2, but in 2009 exacted revenge by beating the Revolution 2–1 before losing to D.C. United 1–2 in 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. Harrisburg next defeated the Red Bulls 3-1 to advance to the quarterfinals, where they lost to the Philadelphia Union by a 5-2 scoreline. In 2012, the City Islanders again won the cash prize for advancing further than any USL-PRO team in the tournament by virtue of a tie-breaker.
The City Islanders have hosted several exhibition matches, or friendlies, against international and top-flight competition. A partnership with D.C. United of Major League Soccer created the "Clash of the Capitals," annual matches between the two capital cities held in 2005–06. In the inaugural edition of the competition in 2005, D.C. United won 1–0 in front of over 4,000 fans at the Skyline Sports Complex. 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. That same year included the City Islanders' first international exhibition, as the club defeated Jamaica's Village United F.C. 5–1 at Hersheypark Stadium.
As part of their affiliation, the City Islanders host annual friendly matches against the Philadelphia Union of Major League Soccer. In 2010, the teams played to a 1–1 draw, with Danny Mwanga giving the Union a lead in the 30th minute before an own goal allowed Harrisburg to equalize a minute later. J.T. Noone appeared for both clubs in the match, playing the first half for the City Islanders before switching jerseys and completing the second half for Philadelphia. The Union prevailed in the 2011 edition by a 5–3 scoreline. 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. With both teams fielding numerous reserves, the City Islanders won the 2012 rematch, which was played at Hersheypark Stadium. 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.
The Harrisburg City Islanders have two of their own supporters groups, the City Island Hecklers (CI Hecklers) founded by "The Heckler", and the Sons of the Susquehanna (SOS) founded by Tyler A. Knupp. The CI Hecklers often position themselves behind one goal, while the Sons of the Susquehanna position themselves behind the other goal. In addition to these two, members of the Sons of Ben (supporters of the Philadelphia Union) also provide support.
The "SOS" attend the City Islanders vs Union friendly at Hersheypark Stadium
Most City Islanders home matches are broadcast live on Invica, with tape delay feeds on ABC 27 Weather Channel, Comcast channel 245 and Verizon Fios channel 462. Additionally, many road games are broadcast through USLLive. Michael Bullock covers the team for the Patriot-News, while Derek Meluzio provides commentary and videos from his Upper 90 blog. The column Confessions of a Soccer Nobody appears regularly in the Sports 'Burger, offering additional coverage and insight.