From 1990 he was featured in Cirque du Soleil's production Nouvelle Expérience, touring for 19 months through Canada and the USA and playing for another year in Las Vegas. With his antics, including stepping through, on and over much of the crowd and the staging of a mock silent-movie melodrama with four members of the audience, he may be the best-remembered of the Cirque's clowns.

The production was filmed for HBO and Shiner's popularity rendered him film roles as a clown in Lorenzo's Oil and as straight man to Bill Irwin in Sam Shepard's Silent Tongue. He and Irwin then created the two-man, wordless show Fool Moon, featuring music by the Red Clay Ramblers, which had also performed in Silent Tongue. This "evening of inspired lunacy" ran from 1992 to 1999, including three separate runs at Broadway. The show won a special Tony for "Live Theatrical Presentation" in 1999, a Drama Desk Award for Unique Theatrical Experience, and an Outer Critics Circle "Special Achievement" Award.

In 2000 he initiated the role of Cat in the Hat, the host and guide of the Broadway stage musical Seussical. Later he toured Europe and Seattle with his shows David Shiner in the Round and Drop Everything. Shiner, who lives in Germany, has further made several appearances on The Tonight Show and is a guest director at the Wintergarden Theatre in Berlin and the Apollo Theatre in Düsseldorf. He has mentored and guest directed for LILALU, a German youth circus program.

In 2007, Shiner wrote and directed Cirque du Soleil's touring production Koozå, using such performers as Gordon White, Jason Berrent, Stephan Laundry, Michael Halvarson, Joshua Zeiner and Christian Fitzherris for the original cast.