The 1998–1999 Obie Awards, honoring distinguished achievement in Off-Broadway and Off-Off-Broadway productions, were presented on May 17, 1999, at New York's Webster Hall.
| Best Production: | The Wooster Group, House/Lights |
| Playwriting: | W. David Hancock, The Race of the Ark Tattoo; |
| Dare Clubb, Oedipus; |
| Christopher Durang, Betty's Summer Vacation |
| Direction: | Jim Simpson, Benten Kozo; |
| Melia Bensussen, The Turn of the Screw; |
| Nicholas Martin, Betty's Summer Vacation; |
| Declan Donnellan, Le Cid |
| Performance: | Liev Schreiber, Cymbeline; |
| Kathleen Chalfant, Wit; |
| Daniel Gerroll, sustained excellence of performance; |
| Matthew Maher, The Race of the Ark Tattoo; |
| Randall Duk Kim, sustained excellence of performance; |
| Mina Bern, sustained excellence of performance; |
| Darius de Haas, Running Man; |
| Viola Davis, Everybody's Ruby; |
| Kristine Nielson, Betty's Summer Vacation; |
| Swoosie Kurtz, The Mineola Twins |
| Design: | Thomas Lynch, for sustained excellence of set design; |
| Michael Chybowski, for sustained excellence of lighting design; |
| Martin Pakledinaz, costume design for The Misanthrope; |
| Diedre Murray, score for Running Man |
| Special Citations: | Peggy Shaw, Menopausal Gentleman; |
| Richard Maxwell, House; |
| Carmelita Tropicana; |
| David Cale, Lillian; |
| Kim Hughes, Sakina's Restaurant; |
| Aasif Mandvi, Sakina's Restaurant; |
| Ronnie Burkett; Tinka's New Dress; |
| Lisa Kron; 2.5 Minute Ride; |
| Basil Twist; Symphonie Fantastique |
| Sustained Achievement: | Wynn Handman |
| Ross Wetzsteon Award: | Ellie Covan-Dixon Place |
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