He then began a career in coaching with the Northern Ireland national football team (under 17s) and English league side Tranmere Rovers (head of youth development).
[2] After a spell with BEC Tero Sasana, Shiels managed League of Ireland club Derry City for three years.
Two days later he was asked to return for a single match and then following this the board decided to endorse Shiels' management for the rest of the season.
[9] This was to be the high-water mark of Shiels' time at Coleraine as the club began to slip back into a more mid-table position, despite some comparatively heavy investment in playing staff.
[9] During the 1999–2000 season, things came to a head when the club lost consecutive matches to Limavady United in the Gold Cup and Linfield in the league, causing Shiels to tender his resignation.
[9] According to the official club website Shiels was manager of Moyola Park from January 1999 to December 2000,[10] although these dates overlap in part with his time at Coleraine.
[14] Shiels responded by making a number of big name signings, including Tommy Wright, Paul Beesley and Liberian international Leon Browne, but none of them proved a success and the club finished in fifth place.
[14] The club improved significantly in the 2002–03 season, although ultimately they managed only second place in the First Division, as well as the Ulster Cup and the Country Antrim Shield.
[14] With Nigel Jemson added to the side Shiels' Braidmen proved a hit in the top flight, finishing sixth and qualifying for the Intertoto Cup.
[14] Shiels again signed some big names, bringing in Rory Hamill, Gary Smyth, Gordon Simms and Tim McCann but the club failed to make any headway.
He left Tranmere in June 2010 to become assistant manager to Mixu Paatelainen at Scottish Premier League club Kilmarnock.
[23] Shiels helped Kilmarnock achieve their first home win against Rangers in 17 years on 27 November 2011, in a 1–0 victory at Rugby Park, with a Manuel Pascali goal in the 80th minute.
[30] On 18 March 2012, Shiels' Kilmarnock side travelled to Hampden Park for the Scottish League Cup Final, where they upset the odds by beating Celtic 1–0, with Dieter van Tornhout scoring the crucial goal in the 83rd minute.
Killie's joy was tempered by the death of Liam Kelly's father, Jack, who suffered a fatal heart attack at the final whistle of the game.
[31] He then told BBC Scotland's Jonathan Sutherland, winning the cup is "unbelievable",[32] in addition "a great emotion" for the Kilmarnock supporters.
[39] A week later, Shiels would accuse referee Euan Norris of making inappropriate comments, following a 2–1 defeat against Inverness Caledonian Thistle, in which Kilmarnock goalkeeper Cammy Bell was sent off.
[49] At the end of the 2012–13 season, with the club finishing in ninth place, and enduring their worst home record in more than 30 years, Shiels future at Kilmarnock was in doubt and after making comments regarding Celtic in a radio interview, he received a further four-game touchline ban.
However, unlike his time at Kilmarnock, Shiels says he would instead keep himself distant from giving match-day interviews on advice from his doctor and leave this to his assistant manager David Hopkin.
[59] Despite making several signings, the club, remained bottom of the league and after a 2–0 loss to Alloa Athletic on 12 April 2014 Morton's relegation was confirmed.
[67] In April 2021 he led the team to a 4–1 aggregate win over Ukraine in the UEFA Women's Euro 2022 qualifying play-offs, securing Northern Ireland's qualification for the final tournament in England.