The 21-year-old, who can operate in central defence and at right-back, has since gone to make 82 appearances for the Merseyside club.
Stones played 28 times for Everton last term with his only goal of the season coming in the 3-0 home win over Manchester United in April.
The defender has represented England at various youth levels and was named on Roy Hodgson’s standby list for last year’s World Cup in Brazil.
His fine form last season saw him make his full England debut in the 3-0 friendly win over Peru at Wembley Stadium last May.
Stones was handed Everton’s iconic number five shirt earlier this week – a number worn by former stalwart Dave Watson.
The young defender helped Everton reach this weekend’s Barclays Asia Trophy final after starting Thursday’s penalty shoot-out win against Stoke.