Fonte was called up to the Portuguese under-21 squad for the Vale do Tejo tournament in 2006.
On 24 January he played against Slovenia, as the match ended with a penalty shootout loss after a 1–1 draw.

On 3 October 2014, at nearly 31, Fonte received his first call-up to the full side, for a friendly with France and a UEFA Euro 2016 qualifier against Denmark.
He made his debut in another exhibition game, playing the second half of a 1–0 win over Argentina at Old Trafford on 18 November.

Fonte was selected by manager Fernando Santos for his Euro 2016 squad.
His first game in the tournament took place on 25 June, as he started alongside Southampton teammate Cédric Soares in the round-of-16 clash against Croatia (1–0 triumph after extra time); he went on to retain his position until the final, won at the expense of hosts France.

Fonte was named in Portugal's final 23-man squad for the 2018 FIFA World Cup in Russia.
Fonte was called up to the Portuguese under-21 squad for the Vale do Tejo tournament in 2006. On 24 January he played against Slovenia, as the match ended with a penalty shootout loss after a 1–1 draw.
On 3 October 2014, at nearly 31, Fonte received his first call-up to the full side, for a friendly with France and a UEFA Euro 2016 qualifier against Denmark. He made his debut in another exhibition game, playing the second half of a 1–0 win over Argentina at Old Trafford on 18 November.
Fonte was selected by manager Fernando Santos for his Euro 2016 squad. His first game in the tournament took place on 25 June, as he started alongside Southampton teammate Cédric Soares in the round-of-16 clash against Croatia (1–0 triumph after extra time); he went on to retain his position until the final, won at the expense of hosts France.
Fonte was named in Portugal's final 23-man squad for the 2018 FIFA World Cup in Russia.
José Fonte