Mitogen-activated protein kinase (MAPK) cascades are important signal transduction mechanisms that connect plant cellular and nuclear responses, which play key roles in plant development and stress responses. Here, the novel MAPK kinase (MAPKK) gene MAPKK1 was isolated from Panax notoginseng (Burk) F.H. Chen. Exogenous methyl jasmonate (MeJA), salicylic acid (SA), ethylene, and hydrogen peroxide treatments induced the transcription level of PnMAPKK1 in P. notoginseng roots. Additionally, PnMAPKK1 expression actively responded to Fusarium solani infection, a major causal agent of P. notoginseng root rot disease. The PnMAPKK1 gene was further fused with the green fluorescent protein gene in a plant expression vector and transformed into onion (Allium cepa) epidermal cells. Laser scanning confocal microscopy confirmed that the PnMAPKK1 protein localized in the cytoplasm. In addition, the plant overexpression vector pCAMBIA2300s-PnMAPKK1 was constructed and transformed into tobacco (Nicotiana tabacum L. cv. Xanthi). The PnMAPKK1 transgenic tobacco lines showed much stronger resistance levels to F. solani infection than the wild type. Moreover, the JA and SA contents in the PnMAPKK1 transgenic tobacco lines were significantly higher than those in wild type during F. solani infection. The up-regulation of several marker genes (PAL4, PR1c, WRKY1, Defensin, and LOC4) involved in JA and SA signaling was correlated with the overexpression of PnMAPKK1 in tobacco. Thus, the PnMAPKK1 gene is a positive regulator of defense responses to F. solani in P. notoginseng.