Despite recent therapeutic breakthroughs, cancer patients continue to face high recurrence and mortality rates due to treatment resistance. Cancer stem cells (CSCs), a subpopulation with self-renewal capabilities, are key drivers of refractive disease. This review explores the application of molecular imaging techniques, such as PET and SPECT, for the noninvasive detection of CSCs. By providing real-time monitoring of CSCs, these imaging methods have the potential to predict therapy resistance and guide personalized treatment approaches. Here, we cover the biological characteristics of CSCs, mechanisms of therapy resistance, and the identification and targeting of CSC-specific biomarkers with molecular imaging. Additionally, we address the challenges and opportunities for the clinical translation of CSC imaging, highlighting strategies where CSC imaging can be used to improve patient outcomes.