| Player | Reason | From | Until | Days | Games missed |
|---|---|---|---|---|---|
 Unknown player | Muscular Problems | 16 Mar 2017 | 23 Mar 2017 | 7 | 1 |
 Unknown player | Hamstring Injury | 23 Feb 2017 | 30 Mar 2017 | 35 | 6 |
 Unknown player | Back Problems | 16 Feb 2017 | 20 Feb 2017 | 4 | 1 |
 Unknown player | Leg Injury | 13 Feb 2017 | 2 Mar 2017 | 17 | 4 |
 Luka Modrić | Muscular Problems | 23 Jan 2017 | 9 Feb 2017 | 17 | 2 |
 Unknown player | Muscular Problems | 23 Jan 2017 | 9 Feb 2017 | 17 | 2 |
 Unknown player | Torn Muscle Fiber | 19 Jan 2017 | 9 Feb 2017 | 21 | 3 |
 Unknown player | Calf Injury | 9 Jan 2017 | 9 Feb 2017 | 31 | 6 |
 Isco | Muscular Problems | 9 Jan 2017 | 16 Jan 2017 | 7 | 2 |
 Lucas Vázquez | Torn Muscle Fiber | 19 Dec 2016 | 12 Jan 2017 | 24 | 2 |
 Mateo Kovacic | Ankle Injury | 19 Dec 2016 | 12 Jan 2017 | 24 | 2 |
| Unknown player | Muscular Problems | 19 Dec 2016 | 12 Jan 2017 | 24 | 2 |
| Unknown player | Calf Injury | 19 Dec 2016 | 2 Feb 2017 | 45 | 8 |
| Unknown player | Muscular Problems | 28 Nov 2016 | 5 Dec 2016 | 7 | 2 |
| Unknown player | Meniscus Irritation | 24 Nov 2016 | 28 Nov 2016 | 4 | 1 |
 Unknown player | Ankle Injury | 24 Nov 2016 | 16 Feb 2017 | 84 | 17 |
 Álvaro Morata | Achilles Tendon Problems | 17 Nov 2016 | 5 Dec 2016 | 18 | 5 |
 Unknown player | Hairline Crack In Foot | 7 Nov 2016 | 5 Dec 2016 | 28 | 5 |
 Unknown player | Muscular Problems | 3 Nov 2016 | 17 Nov 2016 | 14 | 1 |
| Unknown player | Hamstring Injury | 31 Oct 2016 | 24 Nov 2016 | 24 | 4 |
| Unknown player | Muscular Problems | 31 Oct 2016 | 7 Nov 2016 | 7 | 2 |
| Unknown player | Flu | 31 Oct 2016 | 3 Nov 2016 | 3 | 1 |
| Unknown player | Concussion | 27 Oct 2016 | 31 Oct 2016 | 4 | 1 |
| Unknown player | Knee Injury | 10 Oct 2016 | 20 Nov 2016 | 41 | 8 |
| Unknown player | Muscle Injury | 3 Oct 2016 | 17 Oct 2016 | 14 | 1 |
| Luka Modrić | Knee Injury | 29 Sept 2016 | 7 Nov 2016 | 39 | 7 |
| Unknown player | Muscle Injury | 22 Sept 2016 | 13 Oct 2016 | 21 | 3 |
| Unknown player | Minor Knock | 19 Sept 2016 | 26 Sept 2016 | 7 | 2 |
 Unknown player | Fracture Of Fibula Shaft | 19 Sept 2016 | 25 Nov 2016 | 67 | 13 |
| Unknown player | Hip Problems | 15 Sept 2016 | 22 Sept 2016 | 7 | 2 |
 Unknown player | Flu | 15 Sept 2016 | 19 Sept 2016 | 4 | 0 |
| Isco | Ankle Sprain | 25 Aug 2016 | 15 Sept 2016 | 21 | 3 |
| Unknown player | Groin Injury | 11 Aug 2016 | 8 Sept 2016 | 28 | 3 |
| Unknown player | Internal Ligament Strain | 11 Jul 2016 | 8 Sept 2016 | 59 | 7 |
 Unknown player | Heart Problems | 9 Jul 2016 | 1 Jan 2017 | 176 | 30 |
 Unknown player | Achilles Tendon Problems | 2 Jun 2016 | 22 Sept 2016 | 112 | 11 |
| Unknown player | Torn Muscle Bundle | 23 May 2016 | 11 Jul 2016 | 49 | 1 |
| Lucas Vázquez | Knee Bruise | 8 May 2016 | 25 May 2016 | 17 | 2 |
| Unknown player | Achilles Tendon Irritation | 5 May 2016 | 12 May 2016 | 7 | 1 |
| Unknown player | Muscular Problems | 2 May 2016 | 8 May 2016 | 6 | 1 |
| Luka Modrić | Muscular Problems | 2 May 2016 | 9 May 2016 | 7 | 2 |
| Unknown player | Knee Problems | 28 Apr 2016 | 9 May 2016 | 11 | 3 |
| Unknown player | Torn Muscle Fiber | 21 Apr 2016 | 2 May 2016 | 11 | 3 |
| Unknown player | Muscular Problems | 18 Apr 2016 | 25 Apr 2016 | 7 | 2 |
| Unknown player | Minor Knock | 14 Apr 2016 | 18 Apr 2016 | 4 | 1 |
| Unknown player | Thigh Problems | 7 Apr 2016 | 11 Apr 2016 | 4 | 1 |
 Philipp Lienhart | Broken Collarbone | 4 Apr 2016 | 30 May 2016 | 56 | — |
| Unknown player | Calf Injury | 31 Mar 2016 | 11 Apr 2016 | 11 | 3 |
| Unknown player | Flu | 3 Mar 2016 | 7 Mar 2016 | 4 | 1 |
| Luka Modrić | Ankle Injury | 3 Mar 2016 | 7 Mar 2016 | 4 | 1 |
| Unknown player | Hamstring Strain | 29 Feb 2016 | 17 Mar 2016 | 17 | 4 |
| Unknown player | Back Problems | 18 Feb 2016 | 25 Feb 2016 | 7 | 1 |
| Unknown player | Shoulder Injury | 8 Feb 2016 | 15 Feb 2016 | 7 | 1 |
| Unknown player | Foot Injury | 1 Feb 2016 | 29 Feb 2016 | 28 | 5 |
| Unknown player | Calf Muscle Tear | 18 Jan 2016 | 3 Mar 2016 | 45 | 8 |
| Unknown player | Foot Injury | 21 Dec 2015 | 31 Dec 2015 | 10 | 1 |
| Unknown player | Knock | 26 Nov 2015 | 28 Dec 2015 | 32 | 6 |
| Unknown player | Minor Knock | 23 Nov 2015 | 3 Dec 2015 | 10 | 3 |
| Unknown player | Knock | 23 Nov 2015 | 10 Dec 2015 | 17 | 5 |
| Unknown player | Hamstring Injury | 23 Nov 2015 | 7 Jan 2016 | 45 | 9 |
| Unknown player | Minor Knock | 5 Nov 2015 | 16 Nov 2015 | 11 | 1 |
| Unknown player | Adductor Pain | 5 Nov 2015 | 19 Nov 2015 | 14 | 1 |
| Unknown player | Muscle Injury | 26 Oct 2015 | 5 Nov 2015 | 10 | 2 |
| Unknown player | Muscle Injury | 19 Oct 2015 | 5 Nov 2015 | 17 | 4 |
| Luka Modrić | Hamstring Injury | 15 Oct 2015 | 19 Oct 2015 | 4 | 1 |
| Unknown player | Hamstring Strain | 8 Oct 2015 | 16 Nov 2015 | 39 | 6 |
| Unknown player | Shoulder Injury | 5 Oct 2015 | 19 Oct 2015 | 14 | 1 |
| Unknown player | Ankle Injury | 5 Oct 2015 | 19 Nov 2015 | 45 | 6 |
| Unknown player | Leg Injury | 24 Sept 2015 | 22 Oct 2015 | 28 | 5 |
| Unknown player | Muscle Injury | 17 Sept 2015 | 28 Sept 2015 | 11 | 3 |
| Unknown player | Shoulder Injury | 17 Sept 2015 | 2 Oct 2015 | 15 | 4 |
| Unknown player | Torn Muscle Bundle | 10 Sept 2015 | 2 Nov 2015 | 53 | 11 |
| Unknown player | Lung Contusion | 10 Sept 2015 | 8 Oct 2015 | 28 | 7 |
| Unknown player | Muscle Strain | 3 Aug 2015 | 27 Aug 2015 | 24 | 2 |
| Luka Modrić | Knee Injury | 19 Apr 2015 | 30 Jun 2015 | 72 | 9 |
| Unknown player | Inner Ligament Injury | 16 Apr 2015 | 7 May 2015 | 21 | 6 |
 Unknown player | Leg Injury | 6 Apr 2015 | 21 Aug 2015 | 137 | — |
| Unknown player | Hamstring Injury | 26 Mar 2015 | 9 Apr 2015 | 14 | 2 |
| Unknown player | Torn Muscle Bundle | 6 Feb 2015 | 12 Mar 2015 | 34 | 7 |
| Unknown player | Metatarsal Fracture | 5 Feb 2015 | 2 Apr 2015 | 56 | 9 |
| Isco | Muscular Problems | 19 Jan 2015 | 29 Jan 2015 | 10 | 1 |
| Unknown player | Bruised Ribs | 15 Jan 2015 | 16 Feb 2015 | 32 | 7 |
| Unknown player | Calf Injury | 8 Dec 2014 | 15 Dec 2014 | 7 | 2 |
| Luka Modrić | Hamstring Injury | 17 Nov 2014 | 9 Mar 2015 | 112 | 23 |
 Unknown player | Fitness | 7 Nov 2014 | 1 Dec 2014 | 24 | 4 |
| Unknown player | Hamstring Injury | 20 Oct 2014 | 30 Oct 2014 | 10 | 3 |
| Unknown player | Thigh Problems | 6 Oct 2014 | 23 Oct 2014 | 17 | 2 |
| Unknown player | Hamstring Injury | 18 Sept 2014 | 29 Sept 2014 | 11 | 3 |
| Unknown player | Hamstring Strain | 8 Sept 2014 | 18 Sept 2014 | 10 | 2 |
| Unknown player | Thigh Problems | 25 Aug 2014 | 11 Sept 2014 | 17 | 2 |
 Unknown player | Knee Problems | 16 May 2014 | 26 May 2014 | 10 | 2 |
| Unknown player | Calf Injury | 8 May 2014 | 9 Jun 2014 | 32 | 3 |
| Unknown player | Inflammation In The Knee | 8 May 2014 | 13 May 2014 | 5 | 1 |
| Unknown player | Muscular Problems | 8 May 2014 | 22 May 2014 | 14 | 2 |
 Unknown player | Groin Injury | 8 May 2014 | 15 May 2014 | 7 | 1 |
| Unknown player | Muscle Injury | 5 May 2014 | 15 May 2014 | 10 | 2 |
| Unknown player | Muscle Fiber Tear | 3 Apr 2014 | 21 Apr 2014 | 18 | 4 |
| Unknown player | Stomach Flu | 31 Mar 2014 | 3 Apr 2014 | 3 | 1 |
| Unknown player | Torn Muscle Fiber | 31 Mar 2014 | 17 Apr 2014 | 17 | 5 |
| Unknown player | Cruciate Ligament Tear | 19 Mar 2014 | 6 Nov 2014 | 232 | 34 |
