Joseph was drafted fourteenth overall in the 2002 MLS SuperDraft by the New England Revolution, but did not join the team until the 2003 season, having spent much of 2002 searching for a club overseas and later playing for the New York Freedom of USL D-3 Pro League.
Upon joining the Revolution, Joseph quickly proved himself to be one of the most talented defensive midfielders in the league.
He was named to the MLS Best XI in 2005.

In August 2006, Joseph had a $1 million offer from Celtic F.C., but MLS rejected the offer.
In January 2007, another offer of $2 million from Celtic was also rejected by MLS.

In 2008, he started and played the entire MLS All-Star Game versus West Ham United.
The All-stars won that game 3–2, making them 5–0 all time against foreign teams.

He became the Revolution's captain in 2010 after previous captain Steve Ralston left the Revolution to join AC St. Louis.
Later in 2010, Joseph took a leave of absence from the team while he was involved in the Major League Soccer substance abuse and behavioral health program.
Joseph returned to the Revolution at the end of May.
The Revolution signed Joseph to a Designated Player contract for the 2012 season.
On August 1, 2012, Joseph was traded to Chivas USA in exchange for Blair Gavin, a second round pick in the 2013 MLS SuperDraft, and allocation money.

On February 19, 2013, Joseph was traded to Seattle Sounders FC along with second round picks in the 2014 MLS SuperDraft and 2015 MLS SuperDraft, and a swap in allocation order.

In April 2014, Joseph rejoined the New England Revolution.

On May 21, 2016, Joseph signed up to play with Premier Development League side FC Boston.
Joseph was drafted fourteenth overall in the 2002 MLS SuperDraft by the New England Revolution, but did not join the team until the 2003 season, having spent much of 2002 searching for a club overseas and later playing for the New York Freedom of USL D-3 Pro League. Upon joining the Revolution, Joseph quickly proved himself to be one of the most talented defensive midfielders in the league. He was named to the MLS Best XI in 2005.
In August 2006, Joseph had a $1 million offer from Celtic F.C., but MLS rejected the offer. In January 2007, another offer of $2 million from Celtic was also rejected by MLS.
In 2008, he started and played the entire MLS All-Star Game versus West Ham United. The All-stars won that game 3–2, making them 5–0 all time against foreign teams.
He became the Revolution's captain in 2010 after previous captain Steve Ralston left the Revolution to join AC St. Louis. Later in 2010, Joseph took a leave of absence from the team while he was involved in the Major League Soccer substance abuse and behavioral health program. Joseph returned to the Revolution at the end of May.
The Revolution signed Joseph to a Designated Player contract for the 2012 season. On August 1, 2012, Joseph was traded to Chivas USA in exchange for Blair Gavin, a second round pick in the 2013 MLS SuperDraft, and allocation money.
On February 19, 2013, Joseph was traded to Seattle Sounders FC along with second round picks in the 2014 MLS SuperDraft and 2015 MLS SuperDraft, and a swap in allocation order.
In April 2014, Joseph rejoined the New England Revolution.
On May 21, 2016, Joseph signed up to play with Premier Development League side FC Boston.
Shalrie Joseph