Scott Neilson played for the Norwich City Under-11s in 1997/98. Scott came from Hertfordshire and later played for Ware (twice) and Hertford Town. He joined Cambridge City at the end of March 2008. He also spent time at Charlton's youth team.

At the beginning of July 2009, Scott joined Norwich on a two week trial. Norwich manager Bryan Gunn said "It's a trial. He's looked sharp and looked fit in the testing. I've not seen him with the ball at his feet at Norwich City yet. That will happen in the course of the next week and then we'll see how it goes. We've got friendly games coming up so it might be an opportunity, if things go well, to get permission from Cambridge City to ask him to play in those games.He's known about this over the course of the summer so it looks as if he's been training hard during the summer.He's a very quick, busy player who can score a goal. He will take people on, get past people, get crosses into the box and again it just shows you if you do scour the lower leagues, there are players there who might just surprise you and make the step up.”

After Norwich decided not to take Neilson on, he joined Derby County on loan playing in two matches for them. He has also been linked with Torquay and Hartlepool. Following a successful trial, Scott signed for Bradford City at the end of Augist 2009 for an undisclosed fee. Scott signed a three-year contract with the Bantams.

In March 2010, Scott returned to Cambridge; this time joining Cambridge United on loan. He made his debut on 6th March 2010, scoring the only goal of the game as Cambridge won at Barrow.

Returning to Bradford, he was sold to Conference big=spenders Crawley in August 2010

Crawley won promotion to the Football League in 2011 and then Neilson scored the winning goal that secured their promotion to League One in May 2012.

On 19th September 2012 he joined Grimsby Town on a three month loan deal. Towards the end of his stay at Blundell Park, Grimsby manager Paul Hurst admitted his desire to sign Neilson on a permanent deal following an impressive loan spell. Following his final game for the club, a 1-0 victory over promotion rivals Wrexham which put Grimsby on top of the table, manager Paul Hurst admitted that it was unlikely that Neilson would be returning to Grimsby despite making him a good offer. Hurst cited the geographical issue, that the player didn't fancy relocating to the north of England. He had played 10 league games, scoring a single goal.

He joined Luton initally on loan on 24th December 2012 before signing permanently on 1st January 2013.

Released by Luton at the end of the 2012/13 season, he joined Grimsby on 13th May 2013.

In February 2015, he moved back south to join Whitehawk.

On 9th August 2016, he signed for their Conference South rivals Hemel Hempstead Town.