Rod Stewart recorded a cover version that became a #3 hit on the Billboard Hot 100 chart after being released as a single in late 1989, and was also a number-one single on the album rock and adult contemporary charts. The song went to number-one in Canada and made the top ten on the UK Singles Chart in 1990. Stewart received a Grammy nomination for the song in the category Best Male Pop Vocal performance. Stewart's cover featured the slide guitar playing of Jeff Beck.

Other artists who have covered "Downtown Train" include Mary Chapin Carpenter, who included it on her debut album Hometown Girl in 1987; and Patty Smyth, who released a version that same year that reached #95 on the Billboard Hot 100. Everything But the Girl produced an acoustic cover of the song, notably used in the final episode of American sitcom How I Met Your Mother.Bob Seger recorded a cover in 1989, but opted not to release it because Stewart's version had been released earlier. On February 28, 2011, Seger finally released his version of the song as a single, which appears on the retrospective album Ultimate Hits: Rock and Roll Never Forgets. The German band The Piano Has Been Drinking included a version of Downtown Train (Rude Jolf) on their 1990 album The Piano Has Been Drinking which consists entirely of cover versions of Tom Waits songs in the Kölsch language (Colognian).

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