On 10 January 2016, following a shock 3–2 defeat to League Two team Oxford United in the FA Cup, Shelvey appeared to become embroiled in a row with one Swansea fan and then appeared to invite the man to meet him outside. Manager Alan Curtis responded stating "we expect more from Jonjo, it is as simple as that".
On 12 January 2016, Newcastle United announced they had signed Shelvey on a five-and-a-half-year deal, for a reported fee of £12 million. Four days later he made his debut in a 2–1 Premier League victory over West Ham United, the first win for the club in seven matches. He was named man of the match for his involvement in the build-up to both of Newcastle's goals.
Shelvey scored his first goal for the club in a 2–0 win against Brighton & Hove Albion on 27 August 2016. In December 2016, Shelvey was banned for five matches after being found guilty of using racially abusive language towards Wolverhampton Wanderers player, Romain Saïss, in a match on 17 September. He was also fined £100,000 and ordered to attend a Football Association education course. He made 47 appearances and scored 5 goals in 2016–17 as Newcastle were promoted to the Premier League after winning the Championship title.