NACs are one of the largest transcription factor families in plants and are involved in the response to abiotic stress. A new stress-responsive NAC transcription factor gene, LpNAC13, was isolated from Lilium pumilum bulbs. The expression of LpNAC13 was induced by drought, salt, cold and ABA treatments. LpNAC13 overexpressing plants were generated to explore the function of LpNAC13 in response to drought and salt stress. Overexpression of LpNAC13 in tobacco displayed a reduced drought tolerance but exhibited an enhanced salt tolerance. The LpNAC13 overexpression plants had decreased antioxidant enzyme activities, content of proline and chlorophyll, increased MDA content under drought condition, the results in the LpNAC13 plants under salt condition were opposite to those under drought condition. The seed germination and root length assays of overexpression of LpNAC13 showed decreased sensitivity to ABA. Functional analyses demonstrate that LpNAC13 plays opposite roles in drought and salt stress tolerance, acting as a negative regulator of drought response but as a positive regulator of salt response in tobacco.