Ask Jeeves told the Wall Street Journal that the ads were annoying to users and unappealing to advertisers.
Despite long being seen as ineffective on consumer sites, the banner has been a staple of internet advertising since the web started to be seen as a commercial arena. The banner, with its distinctive shape, has also shaped the look of many sites with its prominent centre top location dictating homepage layout.
While other sites, including iVillage and America Online, have banned pop-up ads, Ask Jeeves is the first major search engine site to take such a radical step.
Debate about the banner ad and its effectiveness led the Interactive Advertising Bureau to throw its weight behind four new larger sizes of ad last month. The US internet group, whose members include Microsoft and Yahoo!, backed a new larger universal ad size and three others in a move that it said would make banner ads simpler and more cost effective.
Ask Jeeves said the last banner ads would disappear from its site this month, having begun to withdraw them at the end of last year.
The company said it made the move following user testing, which showed that if users weren't annoyed by banner ads they were, worse still, simply ignoring them. It also said that click-through rates were very low for its banners, with only 0.5% of visitors clicking on banner ads.
Last year Ask Jeeves, which uses the PG Wodehouse character Jeeves, said it would also focus on selling sponsored listings.
"We're focused on targeted ads," Steve Berkowitz, president of Ask Jeeves, said.
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