During the 2008 season Ubiparipović appeared in 16 regular season matches and scored his first league goal. On 10 August 2008, Ubiparipović scored the fourth goal in New York's 4–1 victory over league rival D.C. United. During the 2008 MLS Cup Playoffs, he started all of the team's 4 playoff games helping lead the club to the 2008 MLS Cup final. In the 2009 season Siniša made a career-high 23 appearances for Red Bulls.
On 20 March 2010, Ubiparipović started at left wing for Red Bulls in a 3–1 victory against Santos FC, which was the first match played at the new Red Bull Arena.[8] On 12 May 2010 Ubiparipović scored his second goal for New York Red Bulls in a 3–0 victory over New England Revolution in a 2010 Lamar Hunt U.S. Open Cup qualification match.[9]
His contract expired with New York Red Bulls after the 2010 season and he became a free agent. On 2 August 2011 Ubiparipović signed with Montreal Impact of the North American Soccer League. In 10 games with Montreal, Ubiparipović registered three goals and four assists, and was recognized as the club's newcomer of the year.[10] On 1 November 2011, it was announced that Ubiparipović re-signed to continue with the Impact in 2012, the team's first year in Major League Soccer.[11]
On 6 February 2014, Ubiparipović signed with Ottawa Fury FC of the NASL. He was a key player in helping Ottawa to the 2015 NASL fall season title as he scored 5 goals and recorded 8 assists in 26 matches. He later signed with Indy Eleven on 15 December 2015.[12]
On 20 September 2017, Ubiparipović announced that he would retire from football at the end of the 2017 season.[13][14]