Tuberous sclerosis complex (TSC) is a genetic disorder with formation of benign tumors in many different organs. It has attracted increasing attention from researchers to search for therapeutic drugs for TSC patients. Traditional Chinese medicine (TCM) has become an important source for finding antitumor drugs. Trametes robiniophila Μurr. (Huaier) is a kind of officinal fungi in China and has been applied in TCM for approximately 1,600 years. A large number of clinical applications have revealed that Huaier has good antitumor effect. In this study, we have investigated the effects of Huaier aqueous extract on two TSC cell models, including inhibition of proliferation, induction of apoptosis, cell cycle arrest, and anti-metastasis. We demonstrated that Huaier aqueous extract inhibited JAK2/STAT3 and MAPK signaling pathways in a dose-dependent manner. Therefore, based on the low toxicity and the multi-targets of Huaier treatment, Huaier may be a promising therapeutic drug for TSC.