Allen attended St. Joseph High School in Metuchen, New Jersey, between 2004 and 2008 where he played soccer all four years.
Allen played four years of college soccer at Monmouth University between 2008 and 2011.
While at college, Allen appeared for USL PDL side Central Jersey Spartans in 2010 and 2011.
On January 17, 2012, Allen was selected 5th overall in the 2012 MLS Supplemental Draft by Chivas USA. Allen didn't sign with Chivas USA, instead later signing with Danish side Skive IK in February 2013.
Allen returned to the United States and had trials with D.C United, Orlando City, New York Red Bulls, and the New York Cosmos ahead of the 2015 MLS season. During this time, Allen was contacted by New York City FC to train with David Villa before the beginning of the season, which he did with future Red Bull Mike Grella. Allen was not offered a professional contract prior to the 2015 season, taking a job as a youth soccer coach on Staten Island instead.
After a slow start to their inaugural season, New York City FC offered Allen a contract on May 2, 2015. Allen made his NYCFC debut the following day as a substitute in a 3-1 loss to the Seattle Sounders. Allen got his first start the following week in the first Hudson River Derby against the New York Red Bulls, during which he assisted Patrick Mullins on the team's only goal in a 2-1 loss. Allen made 13 starts in 14 appearances during the 2015 season, drifting in and out of favor under manager Jason Kries, who was fired on 2 November 2015 after a disappointing season.
Under new manager Patrick Viera, Allen solidified himself as the first choice right or left back.
On 27 April 2016, Allen scored his first MLS goal in a 1-1 tie against the Montreal Impact. During a match on 15 May 2016 against the Portland Timbers, Allen set up the first goal by playing a 50-yard through ball to striker David Villa. This pass by Allen has been called the one of the 'greatest assists in NYCFC history' by some reporters. Allen recorded his second assist of the season on 29 May against Orlando City, in a performance that would earn him MLS team of the week honors.
RJ finished the season with 6 assists. This was the joint highest total in the league for a defender.As of 7 June 2017
New York City:
MLS Team of the Week:2015: Week 30
2016: Week 13
FIFA Team of the Week:FIFA 2016: Week 42
NYCFC Player of the Month:2016: May
In 2017, Allen became an ambassador for Concave football boot, and always plays with the Concave Aura+ cleats.