Abstract Although androgen receptor (AR)-targeted therapies, such as enzalutamide, initially improve outcomes of prostate cancer (PCa) patients, resistance inevitably develops, partly driven by prostate cancer stem-like cells (PCSCs). However, the molecular mechanisms linking the maintenance of PCSCs to enzalutamide resistance (ENZR) remain incompletely elucidated. Here, we implicate Ca²⁺/calmodulin-dependent protein kinase 1D (CAMK1D) in PCSC-mediated ENZR. CAMK1D was consistently upregulated in PCa with ENZR and contributed to ENZR by enhancing mitophagy in PCa cells both in vitro and in vivo. Mechanistically, CAMK1D promotes the expansion of PCSCs by enhancing mitophagy through activation of the AMP-activated protein kinase (AMPK)/PINK1 signaling pathway, thereby facilitating cellular adaptation. We revealed that CAMK1D interacts with and phosphorylates AMPK at Thr172, which in turn activates PINK1 to modulate mitophagy, ultimately supporting the expansion of PCSCs under enzalutamide treatment. In a mouse orthotopic PCa model, targeting the CAMK1D/AMPK pathway with the siCAM/HLNP nanoformulation suppresses tumor growth by depleting the PCSCs population, achieving a synergistic effect with enzalutamide therapy. Our findings identify CAMK1D as a key regulator of ENZR that maintains stemness by orchestrating mitophagy, thereby establishing mitophagy as an important nexus between CAMK1D-mediated ENZR and AMPK-driven PCSC enrichment. Therapeutically, we developed a CAMK1D-targeted approach that potently reverses ENZR and improves treatment responses.