Aké joined the Chelsea youth system from Feyenoord in 2011, where he played since the age of 12 after joining the club from ADO Den Haag.

Aké made his Premier League début on 26 December 2012 against Norwich City as a 17 year old, replacing Juan Mata in the final stages. He made his first start for the club in the FA Cup on 27 February 2013, in a 2–0 win against Championship side Middlesbrough. He was chosen to start in a defensive midfield position for Chelsea in the second leg of their Europa League quarter-final clash with Rubin Kazan in Russia on 11 April, a match that finished in a 3-2 loss for Chelsea but resulted in a 5-4 aggregate victory. He made his second European appearance for the club on 2 May, replacing David Luiz in the 3-1 second-leg defeat of Basel, securing Chelsea a spot in the Europa League final. Aké was an unused substitute for Chelsea in the Europa League final against Benfica in Amsterdam on 16 May, which Chelsea won 2-1 on the night. He was voted Chelsea's Young Player of the Year on 16 May 2013. He made his first Premier League start for Chelsea on 19 May 2013 in the 2-1 win against Everton and played the whole match on the last day of the season at Stamford Bridge.

On 8 August 2013, Aké signed a new five-year contract with Chelsea which keeps him at the club until 2018.

Nathan has represented Netherlands at U17 and U19 level. He has captained both sides, earning praise for his performances in midfield for the U17s. Ake was selected into both squads that won the UEFA European under-17 championships in 2011 and 2012 in Serbia and in Slovenia respectively.