| 1992 | The Confession of Isobel Gowdie / Tryst | James MacMillan; BBC Scottish Symphony Orchestra, Jerzy Maksymiuk | | 1 |
| 1993 | Veni, Veni, Emmanuel | James MacMillan; Evelyn Glennie | | 1 |
| 1994 | Búsqueda / Visitatio Sepulchri | James MacMillan | 4 | 1 |
| 1995 | Seven Last Words from the Cross | James MacMillan | | 1 |
| 1998 | Veni, Veni, Emmanuel / Tryst | James MacMillan; Colin Currie, Ulster Orchestra, Takuo Yuasa | | 1 |
| 1999 | Tryst / Ì (A Meditation on Iona) / Adam´s Rib / They Saw the Stone had been Rolled Away | James MacMillan | | 1 |
| 1999 | Symphony 'Vigil' | James MacMillan; BBC Scottish Symphony Orchestra, Osmo Vänskä | | 1 |
| 1999 | The World's Ransoming / Cello Concerto | James MacMillan; Raphael Wallfisch, Christine Pendrill, BBC Scottish Symphony Orchestra, Osmo Vänskä | | 1 |
| 2000 | Kiss on Wood | James MacMillan; The Nash Ensemble, Raphael Wallfisch, John York | | 1 |
| 2001 | Mass and Other Sacred Music | James MacMillan; Westminster Cathedral Choir, Martin Baker | | 1 |
| 2002 | Raising Sparks / Piano Sonata | James MacMillan; Jean Rigby, Nash Ensemble, Martyn Brabbins, John York | | 1 |
| 2002 | The Birds of Rhiannon | James MacMillan; BBC Philharmonic, BBC Singers | | 1 |
| 2002 | The Confession Of Isobel Gowdie / Tuireadh / The Exorcism Of Rio Sumpúl | James MacMillan; BBC Scottish Symphony Orchestra, Osmo Vänskä | | 1 |
| 2003 | Into the Ferment / The Berserking / Britannia | James MacMillan; Martin Roscoe, BBC Philharmonic | | 1 |
| 2004 | Cantos Sagrados | Sir James MacMillan, The Elysian Singers & Sam Laughton | | 1 |
| 2005 | Seven Last Words from the Cross | MacMillan; Polyphony, Britten Sinfonia, Stephen Layton | | 1 |
| 2005 | Symphony no. 3 "Silence" / The Confession of Isobel Gowdie | James MacMillan; BBC Philharmonic, James MacMillan | 4 | 1 |
| 2006 | Mendelssohn / MacMillan / Mozart | Mendelssohn, MacMillan, Mozart; Nicola Benedetti, Academy of St Martin in the Fields, James MacMillan | 5 | 2 |
| 2006 | A Scotch Bestiary, Piano Concerto No. 2 | James MacMillan; Wayne Marshall, BBC Philharmonic, James MacMillan | | 1 |
| 2006 | MacMillan: The Confession of Isobel Gowdie / Adès: Chamber Symphony / Higdon: Percussion Concerto | James MacMillan, Thomas Adès, Jennifer Higdon; London Philharmonic Orchestra, Marin Alsop, Colin Currie | | 1 |
| 2006 | MacMillan and His British Contemporaries | MacMillan; Choir of New College Oxford, Edward Higginbottom | | 1 |
| 2007 | Britannia | Elgar, Davies, Turnage, Britten, MacMillan; Donald Runnicles, Atlanta Symphony Orchestra | | 1 |
| 2007 | Tenebrae | James MacMillan; Cappella Nova, Alan Tavener | | 1 |
| 2008 | The World's Ransoming / Confessions of Isobel Gowdie | James MacMillan; London Symphony Orchestra, Sir Colin Davis, Christine Pendrill | | 1 |
| 2009 | Quickening; Three Interludes from 'The Sacrifice' | Sir James MacMillan | | 1 |
| 2010 | Visitatio Sepulchri / Sun-Dogs | James MacMillan; Netherlands Radio Choir, Netherlands Radio Chamber Philharmonic, James MacMillan, Celso Antunes | | 1 |
| 2011 | Seraph | Arutiunian, MacMillan, Zimmermann; Alison Balsom | | 2 |
| 2011 | Miserere | James MacMillan; The Sixteen, Harry Christophers | | 2 |
| 2011 | Who are these angels? | James MacMillan; Cappella Nova, Alan Tavener | | 1 |
| 2012 | Veni, Veni, Emmanuel: MacMillan Series, Volume 1 | James MacMillan; Netherlands Radio Chamber Philharmonic, James MacMillan, Colin Currie, Gordon Nikolic | 5 | 1 |
| 2013 | Tenebrae Responsories | MacMillan; Westminster Cathedral Choir, London Brass, Martin Baker | | 2 |
| 2014 | Hymns to Saint Cecilia | Britten, Rose, Jackson, Bennett, Vaughan Williams, MacMillan, Elgar, Bliss, Dyson, Gardner, Howells; The Choir of Royal Holloway, Felicity Lott, Rupert Gough | | 2 |
| 2015 | Oboe Concertos | Ralph Vaughan Williams, James MacMillan; Nicholas Daniel, Britten Sinfonia, James MacMillan | | 3 |
| 2015 | Great Britain | Britten, Harvey, MacMillan, Tavener, Davies; SWR Vokalensemble Stuttgart, Marcus Creed | | 1 |
| 2016 | Since It Was the Day of Preparation | James MacMillan; Hebrides Ensemble, Synergy Vocals, Brindley Sherratt | | 1 |
| 2016 | The Lost Songs of St Kilda | Trevor Morrison, Scottish Festival Orchestra, James MacMillan | | 1 |
| 2017 | Stabat mater | James MacMillan; The Sixteen, Britten Sinfonia, Harry Christophers | | 1 |
| 2018 | String Quartets | MacMillan; Royal String Quartet | | 2 |
| 2019 | One Equal Music | James MacMillan; The Elysian Singers, Sam Laughton | | 1 |
| 2020 | Stabat | Arvo Pärt, Pēteris Vasks, James MacMillan; Choir of Clare College, Cambridge, The Dmitri Ensemble, Graham Ross | | 1 |
| 2020 | Symphony no. 5 "Le Grand Inconnu" / The Sun Danced | James MacMillan; The Sixteen, Britten Sinfonia, Mary Bevan, Harry Christophers | | 1 |
| 2020 | Cantos sagrados | Biebl, Ešenvalds, MacMillan, Musgrave, Tippett, Whitacre; National Youth Choir of Scotland, Royal Scottish National Orchestra, Christopher Bell | | 2 |
| 2020 | Symphony no. 4 / Viola Concerto | James MacMillan; Lawrence Power, BBC Philharmonic, Martyn Brabbins | | 2 |
| 2020 | Tallis: Spem in alium / MacMillan: Vidi aquam | Thomas Tallis, James MacMillan; ORA Singers | | 2 |
| 2021 | Brahms: Symphony no. 4 / MacMillan: Larghetto for Orchestra | Brahms, MacMillan; Pittsburgh Symphony Orchestra, Manfred Honeck | | 3 |
| 2021 | Consecration | Sir James MacMillan; Cappella Nova, Alan Tavener | | 1 |
| 2023 | Overtones | Hosokawa, Cage, Gordon, MacMillan; Eline Groslot | | 1 |
| 2023 | Vaughan Williams / MacMillan / Tavener | Vaughan Williams, Tavener, MacMillan; Choir of Westminster Abbey, Peter Holder, James O’Donnell | | 1 |
| 2023 | Anthems | Elgar, Wesley, Howells, Spicer, Gowers, MacMillan, Bednall, Pott; The Choir of Trinity College Cambridge, Stephen Layton | | 1 |
