MotherwellBefore joining Motherwell's U13's team, Jamie played for Westwood Rovers, Drumchapel Thistle and Clyde. Murphy made his first-team début in the 2006–07 season, and scored his first Motherwell goal from the penalty spot in a 2–0 away win over Hibernian on 22 May 2008.
On 23 July 2009, Murphy scored his first European hat-trick against Albanian minnows Flamurtari in the UEFA Europa League. He agreed an extended contract with Motherwell in May 2010 that ties him to the club until 2013. After scoring in the first leg of Motherwell's 2010–11 Europa League third-round match against Aalesunds FK on 29 July 2010, he became Motherwell's leading goalscorer in European football, breaking the record held by Steve Kirk.
Motherwell accepted an offer from Blackpool in January 2012, but Murphy rejected the proposed transfer. In late December 2012, Sheffield United showed interest and Murphy was subject to a £100,000 bid from the Blades with the possibility of Jordan Chapell and Callum McFadzean going in the opposite direction on loan. However on 27 December it was reported that the Blades had a bid rejected by Motherwell with Murphy dismissing transfer speculation, but a few days later Motherwell boss Stuart McCall confirmed that Murphy has been talking to Sheffield United over a transfer and that Motherwell had accepted a bid of £100,000 which could rise to £250,000. Murphy played his last game for Motherwell on 2 January 2013, having been made captain for the occasion, in a 1–0 loss to Celtic at Celtic Park.