Scottish coach Jim Duffy took over as Norwich City's Assistant Manager on 9th February 2007 replacing Doug Livermore who had resigned with immediate effect. Peter Grant said “We are very fortunate to have secured the services of someone with Jim's vast experience and knowledge of the game. He was an excellent player, he's been an excellent coach north and south of the border and he's got an impressive managerial CV. Other clubs have approached him and that's why it was important for me to get him down here to sell Norwich City and what we're trying to do here to him. Jim's knowledge of the game in England and Scotland is huge and that's going to be a major plus for me and for Norwich City.”

Glasgow-born Duffy's playing career took in Greenock Morton, Dundee and Patrick before he returned to Dundee as player/ manager.

He joined Hibs as manager and coached at Chelsea and Portsmouth before returning to manage Dundee. In 2005/6 he joined the coaching staff at Hearts, but lost his job as Director of Football, along with Graham Rix, in March.

Earlier in 2006/7, he rejected managerial approaches from Cambridge United and Dublin side Bohemians.

Duffy was appoined as Norwich's caretaker manager on 8th October 2007 following the departure of Peter Grant. Three defeats in his period in charge did not help Duffy win the permanent contract in charge of City and following Glenn Roeder's appointment, Duffy left the club.

After working in the media, Duffy was appointed as manager of Scottish Second Division side Brechin City on 9 January 2009. He replaced former Northern Irish international Michael O'Neill who left Brechin to take charge at Irish side Shamrock Rovers. Duffy lasted until late May 2010 when he resigned.

On 8th February 2011, Duffy was appointed manager of Clyde who, at the time of the appointment, were rock bottom of the Scottish Third Division having won only once in the league this season. He replaces Stuart Millar, who was sacked the week before. Duffy said: “I am delighted to become manager of Clyde as it is a club which has played a long and distinguished part in the history of Scottish football. Clyde have had some turbulent times in recent seasons, so we will need everyone to work extremely hard to try to gain a level of respectability. Only once this is achieved can we start to look to a brighter future. I cannot wait to get started.”

On 1st February 2012, Duffy was appointed to Clyde's board. Duffy told his club website: "It is a honour and a privilege to become a director at Clyde. My priority remains the football side of the club and building up its infrastructure, but I will help wherever I can and I look forward to working more closely with the board," said Duffy. Clyde said it was "an important step in bringing greater stability to the club and represents a determination to put a structure in place that optimises the development of Clyde FC. On inviting Jim on to the board, it demonstrates our desire to utilise all of his experience as we work together in taking the club forward."

On 19th May 2014, Duffy moved to his former club Greenock Morton as manager, following Kenny Shiel's resignation following Morton finishing bottom of the Scottish Championship. Duffy says a return to full-time football was the reason he could not resist leaving Clyde to become manager of relegated Morton. "The chairman believes he can sustain full-time football and it is great as I've been part-time for five years with Brechin City then Clyde. So it was too good an opportunity to turn down." He insisted that he had no thoughts of leaving Clyde until Morton's approach. "I was absolutely delighted to be the manager of Clyde. We had made an awful lot of inroads into taking the club to a different level at all levels and I think we had managed to do that. Financially, the club was in a much more stable position." Duffy had taken Clyde to the Scottish League One play-offs before losing on penalties in the semi-final against East Fife

Duffy was sacked on 29th April 2018 after a run of defeats saw Morton fail to make the Scottish Premiership playoffs, finishing 7th in the Championship.

Duffy was appointed Dumbarton manager in October 2018, following the sacking of Stephen Aitken. He took them to sixth place in the Scottish League One, losing just twice in their final 15 games.

In June 2020 Duffy had a heart attack. The following month in an open letter to fans, he also thanked NHS staff and well wishers for their support."I aim to return to my work in football at the first opportunity when doctors are happy for me to do so. While my recovery process is not yet complete, I am continuing to rest and recuperate at home with my family around me, and everything is on track.As the date of the new season commencing draws nearer, we will work to ensure we have a squad ready to compete in the campaign ahead. You will of course be kept informed of developments in that process as they happen.It will be a special day when we are able to welcome you back to support us, and after your kindness in the last two weeks, I hope we can reward you with a good season."

He stepped down as Dumbarton manager on 24th May 2021 with the club saying "a new challenge would suit both parties". In 2020/21 the club narrowly avoided relegation from Scottish League One; beating Stranraer and Edinburgh City in the play-offs. He leaves the club with a record of 33 wins and 18 draws in 94 games.

Duffy then joined Ayr United as assistant to David Hopkin. After Hopkin's departure on 9 September following just three wins in 15 games, Duffy stepped up to become caretaker manager. After a four game unbeaten run, he was given the manager's role on 1st October 2021 until the end of the 2021/22 season. He left the role in December 2021.

On 7th November 2022 he was appointed as manager of Clyde.

Following Clyde's relegation to Scottish League Two at the end of the 2022/23 season, Duffy was moved to a position of Director of Football with the club looking to appoint a head coach to look after the first team. Duffy will combine duties previously filled by a head of football operations and head of recruitment. He left his role as Clyde's Director of Football on 18th August 2023 with immediate effect.