| Player | Reason | From | Until | Days | Games missed |
|---|---|---|---|---|---|
 Aymeric Laporte | COVID 19 | 7 Sept 2020 | 28 Sept 2020 | 21 | 2 |
 Unknown player | Ankle Surgery | 5 Sept 2020 | 4 Apr 2021 | 211 | 46 |
 Unknown player | Knock | 3 Jul 2020 | 10 Jul 2020 | 7 | 2 |
 Unknown player | Knee Injury | 23 Jun 2020 | 16 Oct 2020 | 115 | 17 |
 John Stones | Ankle Injury | 19 Jun 2020 | 27 Jun 2020 | 8 | 2 |
 Eric García | Head Injury | 17 Jun 2020 | 29 Jun 2020 | 12 | 3 |
 Kevin De Bruyne | Back Injury | 2 Mar 2020 | 10 Mar 2020 | 8 | 2 |
| Aymeric Laporte | Hamstring Injury | 27 Feb 2020 | 15 Jun 2020 | 109 | 3 |
 Unknown player | Muscle Stiffness | 5 Feb 2020 | 27 Feb 2020 | 22 | 2 |
 Unknown player | Hamstring Injury | 2 Feb 2020 | 24 Feb 2020 | 22 | 3 |
 Unknown player | Knock | 23 Jan 2020 | 1 Feb 2020 | 9 | 2 |
| Aymeric Laporte | Knock | 23 Jan 2020 | 20 Feb 2020 | 28 | 3 |
| Unknown player | Foot Injury | 19 Jan 2020 | 18 Feb 2020 | 30 | 4 |
| John Stones | Foot Injury | 19 Jan 2020 | 25 Jan 2020 | 6 | 1 |
| Unknown player | Knock | 5 Jan 2020 | 19 Jan 2020 | 14 | 2 |
 Unknown player | Knock | 31 Dec 2019 | 6 Jan 2020 | 6 | 2 |
| Unknown player | ILL | 30 Dec 2019 | 3 Jan 2020 | 4 | 1 |
 Unknown player | ILL | 30 Dec 2019 | 7 Jan 2020 | 8 | 2 |
 Gabriel Jesus | ILL | 22 Dec 2019 | 28 Dec 2019 | 6 | 0 |
| Unknown player | Meniscus Injury | 10 Dec 2019 | 5 Sept 2020 | 270 | 22 |
| John Stones | Knock | 8 Dec 2019 | 3 Jan 2020 | 26 | 7 |
| Unknown player | ILL | 8 Dec 2019 | 14 Dec 2019 | 6 | 1 |
 Unknown player | Knock | 8 Dec 2019 | 31 Dec 2019 | 23 | 6 |
| Unknown player | Muscle Injury | 24 Nov 2019 | 20 Dec 2019 | 26 | 7 |
| Unknown player | Muscular Problems | 6 Nov 2019 | 22 Nov 2019 | 16 | 2 |
| Unknown player | Knee Injury | 5 Nov 2019 | 17 Nov 2019 | 12 | 2 |
| Unknown player | Muscle Strain | 3 Nov 2019 | 9 Nov 2019 | 6 | 1 |
 Rodri | Muscle Tear | 22 Oct 2019 | 9 Nov 2019 | 18 | 5 |
| Unknown player | Knee Surgery | 18 Oct 2019 | 14 Dec 2019 | 57 | 13 |
| Unknown player | Knock | 10 Oct 2019 | 21 Oct 2019 | 11 | 1 |
 Unknown player | Knock | 7 Oct 2019 | 28 Oct 2019 | 21 | 2 |
| Unknown player | Hamstring Injury | 2 Oct 2019 | 18 Oct 2019 | 16 | 1 |
| Kevin De Bruyne | Ankle Problems | 29 Sept 2019 | 15 Oct 2019 | 16 | 2 |
| Unknown player | Muscle Fatigue | 19 Sept 2019 | 25 Sept 2019 | 6 | 1 |
| John Stones | Muscle Injury | 17 Sept 2019 | 22 Oct 2019 | 35 | 7 |
 Phil Foden | ILL | 15 Sept 2019 | 25 Sept 2019 | 10 | 2 |
| Aymeric Laporte | Knee Injury | 29 Aug 2019 | 20 Jan 2020 | 144 | 31 |
| Gabriel Jesus | Hamstring Injury | 18 Aug 2019 | 13 Sept 2019 | 26 | 2 |
| John Stones | Muscle Injury | 16 Aug 2019 | 13 Sept 2019 | 28 | 3 |
 Unknown player | Cruciate Ligament Tear | 5 Aug 2019 | 9 Mar 2020 | 217 | 43 |
| Unknown player | Knee Injury | 25 Apr 2019 | 4 Jun 2019 | 40 | 4 |
| Kevin De Bruyne | Hamstring Injury | 21 Apr 2019 | 11 May 2019 | 20 | 3 |
| Unknown player | Knee Injury | 17 Apr 2019 | 17 Sept 2019 | 153 | 17 |
| Unknown player | Knock | 10 Apr 2019 | 15 Apr 2019 | 5 | 0 |
 Bernardo Silva | Knock | 7 Apr 2019 | 14 Apr 2019 | 7 | 1 |
 Unknown player | Fitness | 4 Apr 2019 | 12 May 2019 | 38 | 8 |
| Unknown player | Hamstring Strain | 4 Apr 2019 | 19 Apr 2019 | 15 | 4 |
| Unknown player | Thigh Problems | 31 Mar 2019 | 8 Apr 2019 | 8 | 2 |
 Unknown player | Bruise | 17 Mar 2019 | 8 Apr 2019 | 22 | 3 |
| John Stones | Groin Injury | 5 Mar 2019 | 29 Mar 2019 | 24 | 3 |
| Kevin De Bruyne | Thigh Problems | 2 Mar 2019 | 29 Mar 2019 | 27 | 4 |
| Unknown player | Muscle Injury | 25 Feb 2019 | 30 Mar 2019 | 33 | 5 |
| Aymeric Laporte | Muscle Injury | 25 Feb 2019 | 11 Mar 2019 | 14 | 2 |
| Unknown player | ILL | 21 Feb 2019 | 8 Mar 2019 | 15 | 3 |
| Gabriel Jesus | Hamstring Injury | 18 Feb 2019 | 2 Mar 2019 | 12 | 3 |
| John Stones | Groin Injury | 17 Feb 2019 | 1 Mar 2019 | 12 | 3 |
| Unknown player | Meniscus Injury | 25 Jan 2019 | 27 Feb 2019 | 33 | 8 |
| Unknown player | Knee Injury | 24 Jan 2019 | 3 Apr 2019 | 69 | 14 |
| Unknown player | Muscle Fatigue | 23 Jan 2019 | 4 Feb 2019 | 12 | 4 |
| Unknown player | Muscle Fatigue | 10 Jan 2019 | 22 Jan 2019 | 12 | 2 |
| Unknown player | ILL | 4 Jan 2019 | 13 Jan 2019 | 9 | 2 |
| Kevin De Bruyne | Muscular Problems | 27 Dec 2018 | 2 Jan 2019 | 6 | 1 |
 Unknown player | Knock | 27 Dec 2018 | 2 Jan 2019 | 6 | 1 |
| Gabriel Jesus | Knock | 23 Dec 2018 | 29 Dec 2018 | 6 | 1 |
| Unknown player | Hamstring Strain | 15 Dec 2018 | 28 Dec 2018 | 13 | 4 |
 Unknown player | Injury | 10 Dec 2018 | 22 Dec 2018 | 12 | 3 |
| Unknown player | Hamstring Strain | 9 Dec 2018 | 14 Dec 2018 | 5 | 1 |
| Unknown player | Hamstring Injury | 8 Dec 2018 | 26 Dec 2018 | 18 | 5 |
| Unknown player | Nose Injury | 1 Dec 2018 | 14 Dec 2018 | 13 | 4 |
| Unknown player | Groin Injury | 30 Nov 2018 | 15 Dec 2018 | 15 | 4 |
| Unknown player | Foot Injury | 25 Nov 2018 | 30 Nov 2018 | 5 | 1 |
| Gabriel Jesus | Groin Injury | 25 Nov 2018 | 30 Nov 2018 | 5 | 1 |
| Bernardo Silva | Knock | 19 Nov 2018 | 30 Nov 2018 | 11 | 2 |
| Unknown player | Knee Surgery | 14 Nov 2018 | 21 Jan 2019 | 68 | 15 |
| Unknown player | Achilles Tendon Problems | 10 Nov 2018 | 23 Nov 2018 | 13 | 1 |
| Kevin De Bruyne | Cruciate Ligament Injury | 1 Nov 2018 | 14 Dec 2018 | 43 | 10 |
| Unknown player | Knock | 30 Oct 2018 | 6 Nov 2018 | 7 | 2 |
| Unknown player | Muscle Injury | 28 Oct 2018 | 12 Nov 2018 | 15 | 5 |
| Unknown player | Ankle Injury | 16 Oct 2018 | 29 Oct 2018 | 13 | 2 |
| Unknown player | Groin Injury | 15 Oct 2018 | 25 Oct 2018 | 10 | 2 |
| Unknown player | Hamstring Injury | 3 Oct 2018 | 6 Nov 2018 | 34 | 6 |
| Unknown player | Bruise | 23 Sept 2018 | 31 Oct 2018 | 38 | 7 |
| Unknown player | Hip Injury | 16 Sept 2018 | 24 Sept 2018 | 8 | 2 |
| Unknown player | Foot Injury | 14 Sept 2018 | 7 Oct 2018 | 23 | 6 |
| Unknown player | Achilles Tendon Rupture | 20 Aug 2018 | 3 Apr 2019 | 226 | 47 |
| Kevin De Bruyne | Torn Lateral Knee Ligament | 15 Aug 2018 | 19 Oct 2018 | 65 | 10 |
| Unknown player | Hip Injury | 10 Aug 2018 | 12 Sept 2018 | 33 | 4 |
| Unknown player | Knock | 3 Aug 2018 | 18 Aug 2018 | 15 | 2 |
| Unknown player | Ankle Injury | 5 Jul 2018 | 15 Sept 2018 | 72 | 8 |
| Unknown player | Knock | 10 May 2018 | 15 May 2018 | 5 | 1 |
| Unknown player | Knee Surgery | 7 May 2018 | 26 Oct 2018 | 172 | 17 |
| Unknown player | Knee Injury | 13 Apr 2018 | 27 May 2018 | 44 | 6 |
| John Stones | Adductor Injury | 5 Apr 2018 | 3 May 2018 | 28 | 5 |
| Unknown player | Knee Injury | 11 Mar 2018 | 5 Apr 2018 | 25 | 2 |
| Unknown player | Muscle Injury | 5 Mar 2018 | 31 Mar 2018 | 26 | 2 |
| Unknown player | Hamstring Injury | 26 Feb 2018 | 11 Mar 2018 | 13 | 3 |
| Unknown player | Hamstring Injury | 13 Feb 2018 | 11 Mar 2018 | 26 | 6 |
| John Stones | Knee Problems | 1 Feb 2018 | 4 Feb 2018 | 3 | 1 |
| Unknown player | Injury | 31 Jan 2018 | 11 Feb 2018 | 11 | 2 |
| Unknown player | Torn Ligaments | 29 Jan 2018 | 12 Feb 2018 | 14 | 3 |
