AbstractGlomus tumors are classified as members of the perivascular myoid family of tumors. Nearly half of these show NOTCH‐gene fusions and a smaller subset has BRAF V600E mutations. Here, we report a novel ATG7::RAF1 fusion in malignant glomus tumor occurring in a 40‐year‐old female which has not been reported in the malignant glomus tumor before. A 40‐year‐old female presented with a persistent lateral heel pain and an increase in the size of a mass along the lateral ankle for nearly 10 years. Resected specimen showed a well circumscribed lesion composed of spindled and epithelioid cells with moderate nuclear atypia and mitotic figures (7/10 high‐power fields) including atypical forms without any necrosis, lymphovascular, or perineural invasion. The tumor was positive for smooth muscle actin, smooth muscle myosin heavy chain, H‐caldesmon, collagen type IV, and discovered on gastronintestinal stromal tumors‐1 but negative for AE1/3, desmin, S‐100, CD34, and CD117. RNA sequencing showed presence of ATG7‐RAF1 fusion. This fusion has not been reported in the malignant glomus tumor before. Future studies on larger cohorts are needed to ascertain the biological significance of these tumors with novel gene fusions.