He played for Blackburn’s youth and reserve teams where he scored prolifically, helping the club reach the FA Youth Cup final in 2001, losing 6–3 on aggregate to Arsenal. However his promising career with Rovers was ended due to a ‘serious breach of club discipline’ which was described as ‘totally out of character’ and saw him suspended by the club.

He then joined Bolton Wanderers for a fee of £50,000 following interest from numerous clubs. He played in four Premier League games for Bolton making his professional debut as an 85th-minute substitute in a 2–1 defeat to Charlton Athletic, before signing for Hull City on loan in 2003. On his debut for Hull Walters scored twice in a 5–1 win over Carlisle United. Following his loan spell at Hull, Walters returned to Bolton, where he again went out on loan, this time to Crewe Alexandra however he failed to make an appearance for Crewe due to a tooth infection. In the 2003–04 season he joined Barnsley on loan and played eight league games for the “Tykes”.

Walters qualifies to play for the Republic of Ireland national football team through his Irish mother. He made his international debut for Republic of Ireland U-21 against Switzerland U-21 in October 2003, scoring twice in a 2–0 win. He also played for the Republic of Ireland B team against Scotland B team in 2007. In 2010, Ireland manager Giovanni Trapattoni stated that he could give Walters a call up to the national side in the future. He was called up in November 2010 for the friendly match against Norway and was brought on as a half-time substitute in that game to make his senior international début. Walters was given the nod ahead of Simon Cox in the crucial Play-off game against Estonia and Walters repaid by scoring his first international goal in the 4–0 victory over Estonia in Tallinn in the first leg of the UEFA Euro 2012 qualifying play-offs. On 26 March 2013, Walters scored two goals against Austria before a late strike from David Alaba gave the Austrians a 2–2 draw.

Walters signed for Hull City for a second time in 2004, this time on a permanent transfer. In February 2005, he joined Scunthorpe United on a one-month loan deal and made three appearances for the “Iron”.

He spent the 2005–06 season at Wrexham before he joined their rivals Chester City in 2006. Walters thrived under the management of Mark Wright and scored ten goals in 33 matches. He impressed in an FA Cup tie against Ipswich Town, prompting Ipswich manager Jim Magilton to make a £100,000 bid for Walters, which was accepted.

Walters agreed terms with Ipswich on a deal worth £100,000 plus add-ons in mid-January 2007, having impressed in FA Cup ties between the clubs earlier in the month. He made his debut for Ipswich on 30 January 2007 in a 0–0 draw at Stoke City. Walters scored his first goal for Ipswich in their 2–1 victory over Queens Park Rangers at Portman Road on 3 March 2007. Walters ended the 2006–07 season with goals against Barnsley and a brace on the final day of the season against Cardiff City.

He scored his first ever senior hat-trick in the 6–0 win over Bristol City in November 2007 at Portman Road, in the same week he received a call-up to the Republic of Ireland B squad. On 12 January 2008, he extended his contract with Ipswich until 2011. He had surgery on a niggling knee problem on 19 March 2008 and returned to action against Norwich City on 13 April in half the expected time. Walters played 41 times for Ipswich scoring 13 goals in 2007–08 as the Tractor Boys missed out on a play-off place by just one point. His performances during the season earned him the Player of the Year and Players’ Player of the Year awards.

The 2009–10 season under the management of Roy Keane saw Ipswich struggle to score goals with Walters top-scoring with only eight and Ipswich finished the season in a poor 15th position. In August 2010, Walters expressed to Roy Keane his desire to leave Portman Road after Stoke City made an offer for him.

On 18 August 2010, Walters joined Premier League side Stoke City for an initial £2.75 million fee on a four-year contract. He made his Stoke debut on 21 August 2010 against Tottenham Hotspur. He scored his first goal on 24 August 2010 in a 2–1 Football League Cup win over Shrewsbury Town. He scored his first league goal for Stoke on 2 October 2010 in a 1–0 win over Blackburn Rovers. After the match, Walters earned praise from his former manager Sam Allardyce, and City manager Tony Pulis. In November, Walters scored twice for Stoke in a 3–0 win over West Bromwich Albion, the first goal coming from the penalty spot and the other via a rebound from Scott Carson.

In January 2011, Walters scored twice for City in a 2–0 FA Cup third round replay win at Cardiff City. It took him until the end of March 2011 to find the back of the net in the Premier League again, scoring in a 4–0 win over Newcastle United. He scored in the next match against Chelsea and was named as Man of the Match. Following the match, Tony Pulis spoke of his delight at Walters’ improved performances. “Jon’s come from the Championship and sometimes it takes time to have the confidence and the belief to make the step up. He had an up-and-down start but he’s been fantastic for us. He’s certainly my type of player, he gives everything, he never stops and whatever you’ve paid him, you know he’s earned it.”

Walters scored twice in Stoke’s 5–0 rout over former club Bolton Wanderers in the FA Cup semi-final at Wembley to help Stoke into their first FA Cup Final. Walters described it as the pinnacle of his career. Walters ended the 2010–11 season as joint top goalscorer with Kenwyne Jones, both having scored 12 goals. His first goal against Bolton in the semi-final won Goal of the Season. He played in the 2011 FA Cup Final against Manchester City as Stoke lost 1–0.

Walters played in his first European match on 28 July against Hajduk Split where he scored the only goal in a 1–0 Stoke win. He signed a 12-month contract extension in August 2011. Walters went on to play in 31 matches during the first half of the 2011–12 season scoring seven goals. In March 2012, Walters won the Sir Stanley Matthews Potteries Footballers of the Year award for 2012. Speaking after picking up the award, Walters revealed that he would like to remain at Stoke for the rest of his career. By 21 April 2012, Walters had played in 50 matches during the 2011–12 campaign and scored nine goals of which five were penalties. This led to Walters being criticised by some Stoke supporters but he was backed by his manager. On his 100th appearance for Stoke, Walters scored twice against his old club Bolton Wanderers in a 2–2 draw, a result which relegated the “Trotters”.

Walters continued to be a virtual ever-present in the 2012–13 season as he went on to make a club-record 61 consecutive Premier League starts by 3 November 2012. He scored a well-worked set-piece in a 1–1 draw against West Ham United which earned praise from pundit Gary Neville. He scored twice against Liverpool on Boxing Day 2012 in a 3–1 victory.

On 12 January 2013, whilst playing against Chelsea, Walters scored two own goals becoming only the fourth player to do so in the Premier League, he also missed a penalty in the match as Stoke lost 4–0. He made amends three days later, scoring twice in an FA Cup third round replay victory over Crystal Palace. Walters played in every match in the 2012–13 season and was the club’s top-scorer with 11 goals. The final game of the season against Southampton was his 89th consecutive league start.

Walters made a bad start to the 2013–14 season against Liverpool. After being awarded a last-minute penalty, he saw his shot easily saved by Simon Mignolet and Stoke went on to lose the match 1–0. However, despite this Walters insisted that he would not shy away from taking penalties. On 10 November 2013, Walters featured in his 100th consecutive Premier League match and marked the occasion by scoring in a 3–3 draw with Swansea City. His run of 102 consecutive league starts ended on 4 December 2013 against Cardiff City after picking up an injury. Walters scored a penalty against Arsenal in a 1–0 win on 1 March 2014. He also scored from the spot in the next match against Norwich City but was later sent off for the first time in his career for a high challenge on Alexander Tettey. Walters ended the 2013–14 season with five goals in 36 matches as the Potters finished in 9th position.

Walters opened his account for the 2014–15 season with a brace against Portsmouth in the League Cup. He also scored winning goals against Swansea City, Tottenham Hotspur and Arsenal. On 31 January 2015, Walters became the first Stoke player to score a Premier League hat-trick in a 3–1 victory over Queens Park Rangers. Walters scored his 50th Stoke goal on 24 May 2015 in a 6–1 victory against Liverpool. In total, he scored 11 goals in 36 appearances in 2014–15 as Stoke finished in ninth position for a second consecutive season.

With Walters entering into the final year of his contract, Stoke rejected a bid from Norwich City at the start of the 2015–16 season. Walters vented his frustration with contract talks claiming the club were undervaluing him. This led to him handing in a transfer request but despite this he failed to secure a move away from the club. Walters then scored in back-to-back matches against Leicester City and Bournemouth. Chief executive Tony Scholes stated that he hoped the club could reach a ‘compromise’ with Walters over his contract. His contract dispute was resolved and he signed a new two-and-a-half-year deal with Stoke on 7 November 2015. Walters played 33 times in 2015–16, scoring eight goals as the Potters again finished in ninth position.

Walters scored twice in a UEFA Euro 2016 play-off against Bosnia and Herzegovina on 16 November 2015 to earn Ireland a 2–0 victory and qualification to UEFA Euro 2016.

On 7 July 2017, Walters joined fellow Premier League side Burnley on a two-year contract for a fee of £3 million. He was restricted to just five appearances in the 2017–18 season as he struggled with a recurring knee injury and on his return to action wasn’t able to force his way into Sean Dyche’s plans.

Walters re-joined Ipswich Town, on loan, on 30 August 2018. However, after making only three appearances for the club, Walters was ruled out for six months due to an Achilles injury on 26 September, making him unavailable for the rest of his loan spell at the club.

Walters announced his retirement from football on 22 March 2019 after struggling to recover from his Achilles injury.