The conference was created by Danny Sullivan, founder and former lead editor of Search Engine Watch. The first SES conference was on November 18, 1999 in San Francisco, California and marked the first formal occasion that site owners had met with search engines.

The conference expanded internationally in 2000 when the first SES UK was held in London, England on April 27, 2000, followed by Denmark in 2001, Germany in 2002, and France, Sweden, Canada, Italy and China until 2006. The growth of the industry caused the creation of special niche SES Conferences such as SES Multimedia & Mobile Edition and SES Latino.

The conference is hosted by Incisive Media since 2005 who purchased Search Engine Watch from MecklerMedia (now Jupitermedia) for $43 million that year.

Just over a year after the purchase, Sullivan announced his resignation from guiding the series on August 29, 2006 after a contract dispute but later agreed to run two further shows in the US and speak at a third during 2007.

On June 7, 2007, Kevin Ryan was named as vice president and global content director for the series.