Obesity affects millions of people worldwide and is associated with an increased risk of cognitive decline. The glymphatic system is a brain-wide metabolic waste clearance system, dysfunction of which is linked to dementia. We herein examined glymphatic transport in mice with long-term obesity induced by a high-fat diet for 10 months. The obese mice developed hypertension and elevated heart rate, neuroinflammation and gliosis, but not apparent systemic inflammation. Surprisingly, glymphatic inflow was globally unaffected by the high-fat diet except for the hypothalamus, which displayed increased influx and elevated AQP4 vascular polarization compared to the normal weight control group. We propose that a long-term high-fat diet induced metabolic alteration of hypothalamic neurons and neuroinflammation, which in turn enhanced glymphatic clearance in the effected brain region.