Background: A significant proportion of thymoma patients have concurring autoimmune diseases such as myasthenia gravis (MG). However, the molecular signature of myasthenia gravis-associated thymoma (MGT) is largely unknown. Genomic and transcriptomic profiling of MGT may provide valuable insight to the etiology of MGT and facilitate the development of effective therapeutic approaches. Methods: To study the molecular signature of MGT, 26 thymoma patients were divided into two subgroups according to their clinical presentations. One group included 16 thymoma patients associated with MG (MGT) and the other group had 10 patients without MG (MGF). We profiled the genomic and transcriptomic changes of tumor samples from both subgroups with whole exome sequencing (WES) and RNA sequencing (RNA-seq). Results: The WES results indicated that more genes were mutated in the MGF subgroup than the MGT group, although the difference between two subgroups was not statistically significant. There were only five mutated genes (NBPF1, HRAS, ATAD3B, IFITM3 and MUC4) appeared total mutation frequency exceeded 10%. NBPF1 is the most frequently mutated gene, seen in 25% of the MGTs (4/16) and 10% (1/10) of the MGFs. Neuroblastoma breakpoint family member 1 encoded by NBPF1 was involved in several cancer types including gastric cancer and neuroblastoma, but there is no report on the link of NBPF1 with thymoma or MG. Recent studies showed that NBPF1 is a negative regulator of Akt-p53-Cyclin D and PI3K/mTOR signal pathways. Recurrent mutations in HRAS was only observed in MGFs but not MGTs. Genes mutated in more than one patient were NBPF1, ATAD3B, RPDM9, LOC642131, ADAM21, CGNL1, MUC4 and MUC2 in the MGT subgroup, while only three genes HRAS, CSPG4 and IFITM3 were mutated in more than one patient in the MGF subgroup. Moreover, RNA-seq data identified 106 significantly differentially expressed genes, including 54 upregulated and 52 downregulated genes in the MGT subgroup, further pathway enrichment analysis revealed that the Hippo, Wnt, TGF‐β and focal adhesion signaling pathways were significantly downregulated in the MGT subgroup compared with the MGF subgroup. Conclusions: Our findings provide new insights for the etiology of thymoma with and without MG. mTOR signaling pathway is a key regulator of immune response. Importantly, the protein level of some components in the mTOR pathway was reduced in MG caused-atrophic muscle. Further investigation is warranted to examine the functional roles of NBPF1 in mTOR signaling regulation and the etiology of MG-associated thymoma.