Hypertension is associated with gut dysbiosis and dysregulation of the gut–brain axis. Previous work has shown that probiotic treatments exert beneficial cardiovascular effects in humans and animal models of hypertension. Coupled with the evidence of elevated sympathetic outflow and chronic inflammation in hypertension, we hypothesized that both peripherally and centrally mediated mechanisms underlie the antihypertensive effects of kefir, a probiotic obtained from the fermentation of milk by kefir grains. Eight-week-old spontaneously hypertensive rats (SHRs) were treated by oral gavage with either vehicle or kefir (0.3 ml/100 g/day; 9 weeks; SHR-Kefir), and age-matched with vehicle-treated Wistar Kyoto rats (WKY). Long-term kefir treatment attenuated mean arterial pressure elevations in SHR-Kefir relative to vehicle-treated SHRs. Peripherally, SHRs exhibited differences in the wall of the jejunum (fewer Paneth cells per crypt of Lieberkϋhn and increased tunica muscularis thickness) and higher serum lipopolysaccharide levels compared to WKY, alterations which were reversed in SHR-Kefir. Centrally, kefir treatment reduced IL-6 and TNF-α protein densities, and abolished the microglial activation observed in the hypothalamic paraventricular nucleus and rostral ventrolateral medulla of SHRs. Taken together, our findings indicate that the antihypertensive effects of long-term kefir treatment occur, at least in part, through improved structural and functional integrity of the intestinal wall and protection against neuroinflammation within cardioregulatory nuclei.