Naylor joined Wolverhampton Wanderers upon leaving school in 1996. He made his debut on 12 October 1997, in a 1–0 defeat at Birmingham City. Playing left-back, he went on to establish himself as a first team regular in the following years and was part of the team that won promotion to the Premier League in 2002–03 via the playoffs. He was the Wolves' only ever present player in their Premier League campaign of 2003–04 that saw them relegated. After making the drop, he remained at the club for two further seasons, where he improved further under the management of Glenn Hoddle and attracted the interests of other clubs.
Celtic
Naylor signed for Celtic on 23 August 2006 for £600,000 plus Charlie Mulgrew on a three-year contract and immediately became the team's first choice left back, winning the SPL October Player of the Month award. Naylor's form was recognised with a nomination for the SPFA Player of the Year award for 2007. He won the League and Cup double in his first season with the club and appeared in all of their UEFA Champions League games. He scored his first goal for Celtic with his weaker right foot in a 2–0 win against Hibernian on 1 March 2008, and his second just over a year later; a late left-footed volley to give Celtic a 2–2 draw with Dundee United on 2 March 2009. On 4 May 2010, Naylor scored with an eighth-minute free kick against Old Firm rivals Rangers. He also went on to assist the winning goal, curling a delightful ball into the box to Marc-Antoine Fortuné to head home. Celtic went on to win the match 2–1 with Naylor excelling in his best ever Old Firm performance. Upon the expiration of his Celtic contract in June, Naylor left Celtic.
Cardiff City
In July 2010, Naylor returned to Wolves to keep fit. He spent a week training with Wolves while searching for a new club. On 19 August, he joined Championship side Cardiff City after training with the side for several weeks. He made his debut in a 4–0 win over Doncaster Rovers, coming on for Kevin McNaughton in the 18th minute. He then scored his first goal on 14 September 2010 against Leicester City, after a cross floated into the back of the net. Naylor scored his second goal, against Leeds United, from 25 yards. Naylor was selected less during Cardiff's poor run of the season, in November and December, and eventually dropped for the Swansea City game at Liberty Stadium. Due to the signing of Jlloyd Samuel, Naylor became a last choice left back behind McNaughton and Darcy Blake. On 9 April, Naylor returned to playing, coming on as a half time substitute for Blake, against Doncaster Rovers, then again came on against Sheffield United. He made his last appearance of the season against Reading, coming on for the injured Paul Quinn, in the play-off semi final, first leg. After a disappointing first season at Cardiff City Stadium, new manager Malky Mackay gave Naylor a fresh chance, starting him in all of Cardiff's pre-season games. However, despite this Naylor found himself behind new left back Andrew Taylor, playing his first competitive game under Mackay against Oxford United. His first league appearance came in the absence of injured Andrew Taylor, on 4 December 2011 against Birmingham City. However, despite the good performance, he was again dropped when Taylor returned. After only 6 games under Mackay, Naylor was released from the club at the end of his contract. Following his release, Naylor joined Birmingham City on trial, with a view to a transfer.
On 20 September 2013, Naylor joined League Two side Accrington Stanley on a short-term deal. On 16 January 2014, Naylor had his contract cancelled by mutual consent.
On 27 February 2014, Naylor joined Derby County on short-term deal. With his short-term contract due to expire, he agreed to stay at Derby in a further one-year deal on 25 June 2014.
International career
During his time with Wolves, Naylor also represented the England Under-21s. After his first season with Celtic, England managerSteve McClaren considered Naylor with a call up to the England squad, but injury put paid to his chances and Naylor was not called up.
Personal life
Naylor's brother, Martyn Naylor, is a former professional footballer and is currently a coach for Leamington.