Endosomal Na+, K+/H+ antiporter. Mediates the electroneutral exchange of endosomal luminal H+ for a cytosolic Na+ or K+ (Probable). By facilitating proton efflux, SLC9A9 counteracts the acidity generated by vacuolar (V)-ATPase, thereby limiting luminal acidification. Regulates organellar pH and consequently, e.g., endosome maturation and endocytic trafficking of plasma membrane receptors and neurotransporters.