In 1995, a team called the Puerto Rico Islanders joined the USISL, now the United Soccer Leagues (USL).

The original squad included a large number of local Puerto Rican players as well as a contingent of mainland Americans, Brazilians, Salvadorans and Argentines.

The team played its first league game on April 17, 2004, against the Toronto Lynx at the Juan Ramon Loubriel Stadium, the Islanders lost 1–0 in front of a reported 6,000 fans.

Led by players like Mauricio Salles, Raúl Díaz Arce and Luis Fernando Zuleta Mechura the Islanders finished the 2004 season in 14th place, with a record of 5 wins, 17 losses and 6 ties.

[6] In 2005, the Islanders still under Hugo Hernán Maradona brought in a new group of players that would become staples in the club for the next couple of seasons (Petter Villegas, Marco Vélez, Dan Kennedy, Caleb Norkus, Alejandro González Pareja and Noah Delgado), and retained several key players like Mauricio Salles.

The Islanders opened their 2006 season with a mix of new players like Argentine Gustavo Barros-Schelotto, Chilean Arturo Norambuena, Canadian Alen Marcina, and homegrown talent Marco Vélez, Alexis Rivera Curet, Rafael Ortiz Huertas, and American Dan Kennedy to create one of the strongest lineups in the club's short history, in a serious attempt to take the USL Div.

They also had signed several dangerous players like Panamanian trio Victor Herrera, a Panamanian international, Gustavo Avila, and Alberto Zapata, a new goalkeeper Josh Saunders, rookie Jay Needham,[7] plus a return of players like Marco Vélez, Petter Villegas and Noah Delgado.

It was evident that Toribio Rojas had lost his edge and after an embarrassing 2–1 loss against bottom table Minnesota Thunder was let go from his coaching position and given the post of Youth System Director, when he left the team with a record of 1–3–3.

Acting quickly, the club replaced Rojas with former FC Dallas manager Colin Clarke, who had found himself without a job after the Virginia Beach Mariners went out of business.

He would bring in players like Sandi Gbandi, Jonny Steele, Bill Gaudette, Kendall Jagdeosingh, Osei Telesford among other who would prove key in the race for the regular season title.

After a brief preseason in Florida playing against weaker college sides, the Islanders started the 2008 season with a 1–0 defeat against Portland, the club had a slow start with a record of 1 victory, 2 ties and 3 losses in its first 6 games, but by the end of July the Islanders were on a 5-game victory streak that would lay the foundation for their first Commissioner's Cup run.

On August 8 the club would beat Rochester 4–0 putting them for the first time at the top of the table,[10] a position they would compete for against Vancouver for the rest of the season.

The Islanders would be seeded in the semifinals of the league's Playoffs where they would beat Rochester on an aggregate of 3–2 winning them a spot in the finals against Vancouver.

The Islanders just coming off a successful 2008 season started preparations for 2009 early in February where they traveled to Florida for a group of friendlies against teams like New York Red Bulls, Chicago Fire and the 2008 MLS Champions Columbus Crew.

The club in an attempt to repeat what was achieved the previous year brought back the bulk of the roster with the notable exception of Kenyan International Taiwo Atieno and Salvadorian Edwin Miranda.

Before the CCL's Quarterfinals Clarke, as a way to strengthen the squad brought in midfielder Martin Nuñez from the Carolina Railhawks, defender Kevon Villaroel from San Juan Jabloteh, and striker Sean Fraser from Miami FC.

But most notably Jamaican striker Nicholas Addlery who had an immediate impact on the club scoring 5 goals in his first five games with the Islanders.

During this time they also acquired former Los Angeles Galaxy defender Kyle Veris, midfielder Domenic Mediate, who had just been released from D.C. United, and goalkeeper Chris McClellan formally with the Carolina Railhawks.

[18] This came on the heels of a season where the Islanders were forced to play home games at Bayamon Soccer Complex while Juan Ramón Loubriel Stadium was being renovated and subsequently averaged just 1,864 fans.

In 2006 the Islanders venture into the international stage participating in the CFU Club Championship, in hope of qualifying for the CONCACAF Champions Cup.

This is possible because Puerto Rican football is governed by the Federación Puertorriqueña de Fútbol instead of the United States Soccer Federation.

(Antigua and Barbuda), W Connection (Trinidad and Tobago) and Fruta Conquerors (Guyana), the latter dropped out of the tournament weeks before group play.

This would be the last time the Islanders would play to try to qualify to this incarnation of the confederations top club tournament, since this competition format was abandoned in 2008.

[21] The first leg of the series was played on August 27, 2008, in the Alajuelense home ground, the Estadio Alejandro Morera Soto and in front of 900 spectators, the game ended with a hard-fought 1–1 draw.

ended in a battled 2–2 match which resulted in favor of Islanders FC and qualified them for the final eight of the CONCACAF Champions League.

The Puerto Rico Islanders started the CONCACAF Champions League 2009-10 on July 29, 2009, against Toronto FC in preliminary round action.

The club decided to add a gold star to their logo following the USSF Division 2 Professional League play-off title win in 2010.

On December 8 of 2008, the Finance Vice-President of the club Jorge Pierluisi, established a preliminary meeting with the firm CMA Architects and Engineers along with Positive Impact-Sports and Entertainment Management Consultants to discuss and evaluate improvements to the stadium and the remodeling of such.

It participates in the Puerto Rican 2nd Division, with the goal of developing players from PRISA with extraordinary potential so that they can eventually make the jump to either the Islanders or Bayamón FC.

Populoso was a large bear who wears the same color kit uniform as the Islanders: navy blue, orange, and white.