Ndidi was part of the Nigerian youth setup during his time at Nathaniel Boys of Lagos.
While playing the African U-17 Championship with Nigeria, he was excluded along with two other players from the competition as a precaution, following an MRI age test that suggested he was just slightly above the threshold.
Notwithstanding, he joined up with his teammates in the U-20 team the following year, forming the bedrock of the midfield.
He was called up to the Senior Nigeria national football team on 8 October 2015, making his debut in the friendly game against DR Congo, and playing again a few days later in the 3–0 win against Cameroon, when he replaced John Obi Mikel in the 63rd minute.

He was selected by Nigeria for their 35-man provisional squad for the 2016 Summer Olympics.

In May 2018 he was named in Nigeria’s preliminary 30-man squad for the 2018 World Cup in Russia.
He was included in the African Cup of Nations 2019 squad and played in Nigeria's first match against Burundi.
Ndidi was part of the Nigerian youth setup during his time at Nathaniel Boys of Lagos. While playing the African U-17 Championship with Nigeria, he was excluded along with two other players from the competition as a precaution, following an MRI age test that suggested he was just slightly above the threshold. Notwithstanding, he joined up with his teammates in the U-20 team the following year, forming the bedrock of the midfield. He was called up to the Senior Nigeria national football team on 8 October 2015, making his debut in the friendly game against DR Congo, and playing again a few days later in the 3–0 win against Cameroon, when he replaced John Obi Mikel in the 63rd minute.
He was selected by Nigeria for their 35-man provisional squad for the 2016 Summer Olympics.
In May 2018 he was named in Nigeria’s preliminary 30-man squad for the 2018 World Cup in Russia. He was included in the African Cup of Nations 2019 squad and played in Nigeria's first match against Burundi.
Wilfred Ndidi