New York Red Bulls On December 21, 2015, Allen signed a
Homegrown Contract with the
New York Red Bulls, where he stated in his first interview with the club, "I've waited a long time for this, all my life, but I enjoyed my college career and a lot of my success came from my teammates and my senior class was a big part of my success so I want to thank them. I'm very excited to get started here at the Red Bulls." He joins former
academy and
New York Red Bulls II players,
Derrick Etienne and
Tyler Adams as the third homegrown player signing this season, and adds to a league high of seven on the club for
2016. Allen made his professional debut for
New York Red Bulls II on March 26, scoring two goals in a 2–2 draw against
Toronto FC II. The following week, Allen scored another goal for the club in a 2–0 victory against
Louisville City FC. On May 28, Allen made his first team debut, coming on as a second-half substitute in a 3–0 victory against
Toronto FC. On July 9, Allen scored his first professional hat trick in a 4–2 victory against
FC Montreal. He was later awarded as the USL Player of the Week for his performance. On October 2, 2016, Long scored his sixteenth of the season to help New York Red Bulls II advance to the Eastern Conference Semifinals of the
2016 USL Playoffs in a 4–0 victory over
Orlando City B. In the following match against
Rochester Rhinos, Allen scored two goals, including a 119th minute pk equalizer which sent the match to a penalty shootout, which New York won 5–4 to advance to the Eastern Conference Final of the 2016 USL Cup Playoffs. On October 23, Allen recorded a hat trick and provided an assist in leading New York to a 5–1 victory over
Swope Park Rangers in the
2016 USL Cup Final. For his performance he was named USL Cup Final MVP. On October 18, 2016, Allen was named to the 2016 USL All-League First Team after leading New York with 21 goals in all competitions. On November 3, 2016, it was announced that Allen was voted as the 2016 USL Rookie of the Year. On 6 May 2017, Allen recorded his first two-goal game of the season for
New York Red Bulls II, netting on two penalty kicks, in a 3–1 victory over
Harrisburg City Islanders.
Minnesota United In July 2017, Allen secured a loan move to
Minnesota United FC until the conclusion of the
2017 season. Looking for more playing time, Allen would only register one league appearance for the Loons.
Bethlehem Steel On January 8, 2018, Allen signed with
United Soccer League side
Bethlehem Steel.
Nashville SC On May 22, 2018,
USL side
Nashville SC announced they had paid a transfer fee for Brandon Allen. On November 14, 2018, Nashville announced that they had not re-signed Allen for the 2019 season.
Tampa Bay Rowdies On December 5, 2018, Allen signed with USL Championship side
Tampa Bay Rowdies. Allen scored one league goal for the Rowdies, on April 24, against
Atlanta United 2. Allen also scored in each of the Rowdies two
U.S. Open Cup matches.
Memphis 901 FC On June 26, 2019, Allen was acquired by USL Championship expansion team
Memphis 901 FC. At the time of his signing, Memphis sat last in the league in goals scored.
Oakland Roots On June 28, 2021, Allen signed with USL Championship side
Oakland Roots. ==International career==