Jon Lech Johansen, who cracked the encryption used on DVDs when he was 15, is using the five metre-wide poster to promote software which his company, doubleTwist, has created.
The software allows users to copy songs from their iTunes library onto non-Apple devices.
His ad, which appears to be right outside the Apple store but is actually sitting beside a train station exit, reads: "The Cure for iPhone Envy. Your iTunes Library on any device. In seconds."
The ad was reportedly intended to go up on Monday, coinciding with Apple's Worldwide Developers Conference, which was being held in San Francisco, but it was put up three days early by the ad agency.
It then was removed after one day as Bay Area Rapid Transit (Bart), which operates the train system on which the poster was erected, said it was "too dark" and did not let enough light through.
Johansen published photos of the ad on his blog, showing "plenty of light coming through".
He then submitted the ad on a white background instead, however this was rejected "for having a solid white background".
Johansen said: "Apple is a major Bart advertiser (in the past they've plastered entire Bart stations with iPod ads).
"Apple's WWDC conference ends on Friday. It's pretty obvious what's going on here... I'm sure our ad will conveniently be back up after WWDC ends.
The ad was subsequently reposted by the middle of this week after much campaigning from technology publishers.
Johansen, who is now 25, launched doubleTwist in February 2008. It allows customers to route around digital rights management in music files and convert files between various formats.
This software will be invaluable to consumers without an Apple digital music device because it allows them to get around the restrictions placed on the iTunes store, which prevents its songs being played on non-iPod devices.