The internet programme is in the running for the 'Best Online Drama' prize at the ceremony, which yesterday announced the nominees for its 15th annual show.
Webbys honour excellence on the internet each year, including websites, interactive advertising, online film and video.
EastEnders: E20 made its debut in January 2010, launching a 12-part series which had over 3.3 million requests across the EastEnders website, BBC iPlayer and BBC red button service.
The show is thought to have built on this success with its second run last September, while the third series is due to begin filming in May.
Speaking of E20's Webby nod, producer Deborah Sathe commented: "I am so proud of what we have achieved with EastEnders: E20, and to be nominated for a Webby proves how far the series has come.
"I am so excited that we are on the brink of filming our third series, after having such fun making the first two. I can't wait for the audience to meet the latest batch of characters and watch the new kids rock the Square."
The Webbys are now open to a public vote via the ceremony's official website. Winners will be announced on May 3.