Spinal and bulbar muscular atrophy (SBMA) is caused by polyglutamine (polyQ) expansions in androgen receptor (AR), and is characterized by the degeneration and loss of brainstem and spinal cord motor neurons. Using cellular and animal models, we investigated what kinases and phosphatases target polyQ-expanded AR, whether polyQ expansions modify AR phosphorylation, and how this contributes to neurodegeneration. By taking an unbiased approach, we combined mass spectrometry analysis with kinase and phosphatase small library screening. Mass spectrometry showed that polyQ expansions preserve native phosphorylation and increase phosphorylation at conserved sites controlling AR stability and transactivation. In small molecule screening, we showed that CDC25/CDK2 signaling enhances AR phosphorylation, and the calcium-sensitive phosphatase calcineurin had opposite effects. Pharmacologic and genetic manipulation of these kinases and phosphatases modified polyQ-expanded AR function and toxicity in cells, flies, and mice. Ablation of CDK2 reduced AR phosphorylation in the brainstem and restored expression of Myc and other genes involved in DNA damage, senescence, and apoptosis, indicating that the cell-cycle regulated kinase plays more than a bystander role in SBMA-vulnerable post-mitotic cells.