In 1965 Johnson bought his first Fender Telecaster from a shop in Southend, Essex for £90 (equivalent to £1,599 as of 2016). He still plays a vintage 1962 Fender Telecaster with rosewood fingerboard which he bought in 1974, shortly after Dr. Feelgood signed their first record deal. Originally of sunburst-coloured body with white pickguard, Johnson later refinished it in black and added a red pickguard.

Johnson developed his own image, coupling jerky movements on stage (his so-called "duck walk") with a choppy guitar style, occasionally raising his guitar to his shoulder like a gun, and a novel dress sense (he favoured a black suit and a pudding bowl haircut). He achieved his playing style by not using a pick but instead relying on fingerstyle. This enabled him to play rhythm guitar and riffs or solos at the same time creating a highly percussive guitar sound. It evolved from a failed attempt to copy Mick Green of Johnny Kidd and the Pirates, a Guitarist whom Johnson greatly admired. His style formed the essential driving force behind Dr. Feelgood during their initial years, including the band's first four albums, Down by the Jetty, Malpractice, Stupidity and Sneakin' Suspicion, all released between 1975 and 1977.

In 1977, he was a founding member of Solid Senders, with keyboardist John Potter, Bassist Steve Lewins, and Drummer Alan Platt. They signed to Virgin in 1978 and released the album, Solid Senders that year. The Wilko Johnson Band played at the 'Front Row Festival', a three-week event at the Hope and Anchor, Islington in late November and early December 1977, featuring many early punk rock acts. This resulted in the inclusion of two tracks by The Wilko Johnson Band ("Dr. Feelgood" & "Twenty Yards Behind"), on a hit double album of recordings from the festival. The Hope & Anchor Front Row Festival compilation album (March 1978) which reached number 28 in the UK Albums Chart

In 1980, Johnson joined Ian Dury's band, The Blockheads. Around 1984 he then re-formed The Wilko Johnson Band, joined by Blockhead Bassist Norman Watt-Roy and Italian born Drummer Salvatore Ramundo. 'Sav' Ramundo left the band in June 1999 and was replaced by Steve Monti (future Curve and The Jesus and Mary Chain drummer). Johnson's second album, Ice on the Motorway, was released in 1981, and his EP "Bottle Up and Go!" with Lew Lewis followed in 1983. Several albums were released on European labels over the next decade. In 1992, Johnson appeared at the Eurockéennes music festival, and the following year at GuilFest. The album Going Back Home appeared on the Mystic label in 1998. He began to cut back on his concert appearances in 1999, and released the album Don't Let Your Daddy Know (Live in Japan 2000) the following year.

Johnson lives in Southend. He married his childhood sweetheart Irene Knight when they were teenagers, and the couple had two sons, Matthew and Simon. Johnson was widowed in 2004 after his wife's death from cancer. He is interested in astronomy, painting and poetry. Johnson's son Simon is also a Guitarist, playing in Southend-based band Eight Rounds Rapid.

The studio album Red Hot Rocking Blues was released in 2005. This contained covers of classics by the likes of Van Morrison, Bob Dylan, Ray Charles, Sonny Boy Williamson and Lead Belly. Throughout 2005 and 2006 the band teamed up with The Hamsters and John Otway to take part in 'The Mad, the Bad & the Dangerous' tour. He played Club Bang Bang at the 100 Club on 6 October 2006, and played throughout the UK, Europe and Japan, including twice a year at the 100 Club.

Johnson's musical style underpinned the early years of Dr Feelgood. A style that has been cited as one of the founding influences of the British punk movement. Jean-Jacques Burnel of The Stranglers says "I often say to journalists there is a bridge between the old times and the punk times. That bridge is exclusively the Feelgoods, it allowed us to go from one thing to another. That's the connection, the DNA." This influence was explored in the 2009 documentary about Dr Feelgood, Oil City Confidential. Reviewing Johnson's autobiography, Mark Blake of Q magazine said "In the mid-70s the band's brutish R&B and their guitarist's eye-popping thousand-yard stare inspired a young John Lydon, Paul Weller and Suggs from Madness. Looking Back at Me secures the man born John Wilkinson's reputation as one of British rock's most unique characters. Wilko recalls his childhood on Canvey Island and how he followed the '60s hippy trail to Goa ... before helping invent punk with Dr Feelgood." The BBC4 three-part documentary series Punk Britannia, first aired in May 2012, also stressed the importance of Dr Feelgood as "pub rockers, a generation of bands sandwiched between 60s hippies and mid-70s punks who will help pave the way towards the short, sharp shock of punk".

On 2 October 2010, it was announced that Johnson was to support The Stranglers on their 'Black & Blue' UK tour starting in March 2011. In April 2011, he played several sold out shows as part of the Kilkenny Rhythm & Roots Festival in Ireland.

For his acting debut, Johnson was cast in the role of mute executioner Ser Ilyn Payne, in both the first and second season of the HBO fantasy series Game of Thrones, after the producers had seen him in Oil City Confidential. He related that "'They said they wanted somebody really sinister who went around looking daggers at people before killing them. That made it easy. Looking daggers at people is what I do all the time, it's like second nature to me'." He appeared in four episodes: "The Kingsroad", "Baelor" and "Fire and Blood" (season one, 2011), and "Blackwater" (season two, 2012).

Johnson was forced to cancel a show in November 2012 when he was rushed to hospital with an undisclosed ailment. He was diagnosed in January 2013 with late stage pancreatic cancer, and elected not to receive any chemotherapy.

On 25 January 2013, he gave an interview to John Wilson on the BBC Radio 4 arts programme Front Row. He discussed his cancer, and said doctors had told him he had nine or ten months to live. He talked about his "farewell tour" of the UK set for March, and how his diagnosis had made him feel "vividly alive". After the tour was over, he announced he would spend his final days recording a farewell album with the Who's lead singer Roger Daltrey. The album, Going Back Home, was released in March 2014. "I thought that was going to be the last thing I ever did," he later told BBC News entertainment correspondent Colin Paterson in October 2014.

However, Johnson did not have the more Common adenocarcinoma of the pancreas. It was later discovered that he had a pancreatic neuroendocrine tumor (PNET), a less virulent and more treatable form of the disease. Johnson underwent radical surgery to treat his illness, and the doctors were hopeful that his prognosis would be good. At the Q Awards on 22 October 2014, Johnson accepted the "Icon Award" and announced that he was "cancer-free" having undergone "removal of his pancreas, spleen, part of his stomach, small and large intestines and the removal and reconstruction of blood vessels relating to the liver". Johnson said: "It was an 11-hour operation… This tumour weighed 3kg - that's the size of a baby! Anyway, they got it all. They cured me. It's so weird and so strange that it's kind of hard to come to terms with it in my mind. Now, I'm spending my time gradually coming to terms with the idea that my death is not imminent, that I am going to live on". He added that he was still recovering from the operation and when asked what he would do next replied: "I don't know really".

In February 2017, The Wave Pictures released a vinyl EP titled Canvey Island Baby, which features five covers of Johnson-penned tracks and an additional song, the title track written by the band's singer/guitarist David Tattersall.