Approximately one out of two patients with diabetes develops diabetic neuropathy; of these, 20% experience neuropathic pain. Risk factors for neuropathic pain are largely unknown; however, DNA methylation was recently associated with neuropathies and degeneration of nerve fibers. The aim of this work was to describe the DNA methylation signature and identify genes associated with neuropathic pain in type 2 diabetes mellitus (T2DM). We discovered distinct DNA methylation signatures that differentiate painful and painless neuropathy phenotypes associated with T2DM and identified genes with potential as therapeutic targets for neuropathic pain, such as GCH1, MYT1L, and MED16. This work can serve as reference hallmark for future studies on painful diabetic neuropathy and other chronic pain conditions.