Unlike the year prior, the Rough Riders won their semi 5–2 against the Tampa Bay Cyclones, and then beat Minnesota Thunder 2–1 to win the USISL Championship.

The Rough Riders lost several players to the nascent MLS in 1996, including Meola and Savarese, but went on to have a successful season nevertheless, finishing with an 11–7 record and winning the North Atlantic Division.

The Rough Riders also enjoyed a run to the quarterfinals of the US Open Cup, beating USASA amateur team Bridgeport Italians in the second round, then upsetting Major League Soccer side New England Revolution 4–3 before eventually falling to the New York/New Jersey MetroStars 1–0 on a golden goal.

Fortunes improved significantly in 2000, as the Rough Riders claimed their first regular-season title at this level, winning the Northeast Division by one point over the Rochester Raging Rhinos with a 16–9–4 record.

The Rough Riders bounced back magnificently in 2002, winning the D3-Pro League Atlantic Conference with a 13–6–1 record, six points clear of New York Freedom in second place.

Long Island squeaked past New York on penalty kicks after a 2–2 tie in the playoff quarterfinals, and enjoyed a dominant 3–0 win over the Connecticut Wolves in the semifinal to reach the championship game.

The final against Southern Conference champions Wilmington Hammerheads was a tight game, but the Rough Riders emerged as 2–1 victors to take their second championship in franchise history.

The team enjoyed a couple of comprehensive victories, notably a second 4–1 win over Northern Virginia Royals in which Moussa Sy scored all four goals, and a 5–2 hammering of New Hampshire Phantoms in early July.

The next season was arguably the worst in team history, with the Rough Riders finishing at the bottom of the table with three wins and fifteen goals scored.

Their early season form took them to the US Open Cup for the fourth time, but they exited the competition at the hands of USL First Division stalwarts Rochester Raging Rhinos.

The Rough Riders' first season at this level ended with them fourth in the Northeast Division, nine points behind divisional champs Cape Cod Crusaders, and just out of the playoffs.

In December, the team was invited by the Bermuda Football Association to participate in its BFA Christmas 2010 tour, a holiday tournament for local and international clubs.

In their first playoff appearance in two years, the Rough Riders defeated the New Hampshire Phantoms 3–2 as Dominick Sarlee netted a hat trick in the USL Premier Developmental League's Eastern Conference Championships.

The Rough Riders' postseason continued as they advanced to the PDL Eastern Conference Championship against Mid Atlantic Division rivals Jersey Express.

The semifinal match against the Jersey Express remained scoreless until the 48th minute when Kramer's shot from inside the penalty box put the Rough Riders ahead.

Former Rough Riders player Tim Parker made his Major League Soccer playoff debut for the Vancouver Whitecaps against the Portland Timbers in early November.

Parker also earned his first call-up to the United States National Team training camp in January that included international friendlies versus Canada and Iceland.

Long Island, which finished runner-up in the Northeast Division, defeated Mid-Atlantic winners New York Red Bulls U-23 in an Eastern Conference play-in game.

The offseason was highlighted by midfielder Danny Bedoya signing with New York City FC, Rough Riders' parent club, on August 9.

On April 21, 2016, New York City FC announced the Long Island Rough Riders would be their official Premier Development League affiliate beginning with the 2016 season.