Although chondroid syringoma rarely occurs outside the head and neck, the majority of malignant chondroid syringomas are identified in the extremities. Here, we present a case of atypical chondroid syringoma in the fifth toe. Diagnosis of chondroid syringoma with atypical cells was made following initial excisional biopsy and histology, necessitating repeated surgery for positive margins. In this case report, we examine the radiopathologic correlation of this diagnosis, detail the imaging findings of benign and malignant chondroid syringomas, and highlight how magnetic resonance imaging can be used to guide surgical planning and treatment course of this potentially malignant tumor.