Previous studies have demonstrated the penetration of anthocyanins through the blood−cerebrospinal fluid barrier (BCSF barrier) after intraruminal administration of chokeberry and red cabbage preparation to sheep. However, they have failed to explain which food anthocyanin forms are more capable of crossing the BCSF barrier. Thus, this study aim was to verify the ability of cyanidin 3-galactoside (Cy3gal, main chokeberry anthocyanin) and cyanidin 3-diglucoside-5-glucoside (Cy3diG5G, main red cabbage anthocyanin) to cross the BCSF barrier on the sheep model (n = 16) after intravenous administration (to exclude the influence of gastrointestinal processes) of preparations containing these compounds. The micro-HPLC-MS/MS analysis showed that, after intravenous administration, anthocyanins penetrated the BCSF barrier and that the penetration potential of Cy3gal derivatives (6.73%) was higher than that of Cy3diG5G derivatives (6.10%), suggesting the observed differences to be largely due to the type and number of substituents as well as the size of the molecule.