A former midfielder, Neestrup emerged from the FC Copenhagen youth academy, but saw his career mostly diminished due to injuries.

He was appointed head coach of second-tier 1st Division club Viborg in June 2019, after having worked as an assistant at Copenhagen the season before.

[3] After recovering, Neestrup made his Danish Superliga debut in the last match of the 2006–07 season against Vejle Boldklub.

His stint with the club was not successful, being sidelined for large parts of the season due to injuries and a car accident.

[9] On 12 December 2023, he guided them to the knockout stages of the Champions League, being placed second in a group with Bayern Munich, Galatasaray and Manchester United.