Jonny Mullins was at the Norwich City Centre of Excellence at Potters Bar in the late 1990s until a change of rules by the Football Association forced Norwich to close the Centre due to travelling times.

Joining Reading's Academy, he spent two periods on loan at Kidderminster Harriers. The first from 17th December 2004 until 7th April 2005 in whcih he made 21 appearances scoring twice. The second from 25th October 2005 until the 2nd May 2006 in which he made 30 appearances, again scoring twice.

He was released by Reading in May 2006 and the Harriers expressed interest in signing him although they are facing competiion from Chester City. Instead he signed for Mansfield Town on a two year contract on 1st June 2006. "I wasn't going to be figuring much in the Reading side, so I see the move to Mansfield as nothing but positive," he told the Stags' website. "When the gaffer (Peter Shirtliff) contacted me, I was delighted to come back into league football."

Despite making 49 appearances during 2007/8, scoring three goals, and winning the Player of the Season award, Mullins could not help Mansfield avoid relegation out of the Football League and into the Conference

On 18th June 2008, John agre a two year contract with Stockport County

He moved to Rotherham on 6th July 2010, signing a two year deal.

On 5th October 2012, Mullins joined Oxford on a three month loan. He had not played for the Millers since the 6-2 defeat by Port Vale in September 2012.

Returning to his place in the Rotherham side, he scored in a 2-0 win over Aldershot on 27th April 2013 which secured Rotherham's promotion to League One

On 23rd July 2013, Mullins joined Oxford on a three year contract for an undisclosed fee.

Released by Oxford in May 2016, he signed for Luton on a two year contract on 31st May 2016.

After being released by Luton in May 2018 after helping them win promotion to League One in 2017/18, he signed for Cheltenham on 16th May 2018.

On 17th May 2018 Mullins retired from full-time football by mutual consent, ending a 15-year senior career and a one-year stay with League Two side Cheltenham Town.