| 28 Nov 13 | J. Lundstram John Lundstram | EvertonEVE | → | Yeovil TownYEO | Loan |
| 28 Nov 13 | J. Lundstram John Lundstram | EvertonEVE | → | Yeovil TownYEO | Loan |
| 26 Sept 13 | S. Duffy Shane Duffy | EvertonEVE | → | Yeovil TownYEO | Loan |
| 26 Sept 13 | S. Duffy Shane Duffy | EvertonEVE | → | Yeovil TownYEO | Loan |
| 13 Sept 13 | L. Garbutt Luke Garbutt | EvertonEVE | → | Colchester UnitedCOL | Loan |
| 02 Sept 13 | F. Júnior Francisco Júnior | EvertonEVE | → | VitesseVIT | Loan |
| 02 Sept 13 | M. Fellaini Marouane Fellaini | EvertonEVE | → | Manchester UnitedMAN | 27,500,000 |
| 02 Sept 13 | J. McCarthy James McCarthy | Wigan AthleticWGA | → | EvertonEVE | 13,000,000 |
| 02 Sept 13 | V. Anichebe Victor Anichebe | EvertonEVE | → | West Bromwich AlbionWBA | 6,000,000 |
| 02 Sept 13 | G. Barry Gareth Barry | Manchester CityMNC | → | EvertonEVE | Loan |
| 02 Sept 13 | F. Júnior Francisco Júnior | EvertonEVE | → | VitesseVIT | Loan |
| 02 Sept 13 | R. Lukaku Romelu Lukaku | ChelseaCHE | → | EvertonEVE | Loan |
| 02 Sept 13 | J. McCarthy James McCarthy | Wigan AthleticWGA | → | EvertonEVE | 13,000,000 |
| 25 Jul 13 | C. McAleny Conor McAleny | EvertonEVE | → | BrentfordBRE | Loan |
| 10 Jul 13 | G. Deulofeu Gerard Deulofeu | BarcelonaBAR | → | EvertonEVE | Loan |
| 10 Jul 13 | G. Deulofeu Gerard Deulofeu | BarcelonaBAR | → | EvertonEVE | Loan |
| 09 Jul 13 | A. Alcaraz Antolin Alcaraz | Wigan AthleticWGA | → | EvertonEVE | Free |
| 09 Jul 13 | J. Robles Joel Robles | Atletico MadridATL | → | EvertonEVE | Undisclosed |
| 09 Jul 13 | A. Alcaraz Antolin Alcaraz | Wigan AthleticWGA | → | EvertonEVE | Free |
| 09 Jul 13 | J. Robles Joel Robles | Atletico MadridATL | → | EvertonEVE | Undisclosed |
| 08 Jul 13 | A. Koné Arouna Koné | Wigan AthleticWGA | → | EvertonEVE | Undisclosed |
| 08 Jul 13 | A. Koné Arouna Koné | Wigan AthleticWGA | → | EvertonEVE | Undisclosed |
| 17 Jun 13 | J. Bidwell Jake Bidwell | EvertonEVE | → | BrentfordBRE | Undisclosed |
| 20 Feb 13 | J. Lundstram John Lundstram | EvertonEVE | → | Doncaster RoversDON | Loan |
| 11 Feb 13 | J. Hammar Johan Hammar | EvertonEVE | → | Stockport CountySTO | Loan |
| 31 Jan 13 | M. Gueye Magaye Gueye | EvertonEVE | → | BrestBRES | Undisclosed |
| 31 Jan 13 | M. Gueye Magaye Gueye | EvertonEVE | → | BrestBRES | Undisclosed |
| 31 Jan 13 | J. Stones John Stones | BarnsleyBAR | → | EvertonEVE | Undisclosed |
| 31 Jan 13 | J. Stones John Stones | BarnsleyBAR | → | EvertonEVE | Undisclosed |
| 30 Jan 13 | Anton Forrester | EvertonEVE | → | Blackburn RoversBLK | Free |
| 30 Jan 13 | Anton Forrester | EvertonEVE | → | Blackburn RoversBLK | Free |
| 11 Jan 13 | R. Barkley Ross Barkley | EvertonEVE | → | Leeds UnitedLEE | Loan |
| 11 Jan 13 | R. Barkley Ross Barkley | EvertonEVE | → | Leeds UnitedLEE | Loan |