The cerebral circulatory disorder associated with arterial hypertension results in neuroinflammation, in which microglia and macrophages of the brain are actively involved. The study aimed to assess functional activity and immunophenotype of microglia and macrophages in the areas of brain barriers in spontaneously hypertensive rats (SHR). Specimens of the brain of male Wistar and SHR rats (age 3–4 months, n = 10) were used. The study involved the use of immunohistochemistry analysis and confocal laser microscopy. The presence of М2 activation (CD206) and phagocytic activity (CD68) markers in the population of microglia and macrophages was assessed. It was shown that the CD206 protein was present in perivascular cells, the counts of which were considerably increased in SHR rats (40.69 ± 4.87 cells per 1 mm2 vs. 28.73 ± 1.39 in Wistar rats; t-test, р = 0.0007). The quantitative analysis conducted allowed us to identify the upward trend of the share of phagocytic cells in the brain of SHR rats compared to Wistar rats. No changes in the CD68 protein distribution were found in SHR rats, therefore, activation of microglia and macrophages is not accompanied by the phagocytic activity increase. The findings suggest alternative activation of brain macrophages in neuroinflammation caused by arterial hypertension.