Anthocyanins are natural colorants with antioxidant properties, shown to inhibit photoaging reactions and reduce symptoms of some skin diseases. However, little is known about their penetration through the stratum corneum, a prerequisite for bioactivity. The aim was to investigate anthocyanin penetration from lipophilic cosmetic formulations through the skin using a porcine ear model and human volunteers. ATR-FTIR/PLS regression and HPLC-PDA-MS were used to analyze anthocyanin permeation through the stratum corneum. Penetration of all anthocyanins was evident and correlated with molecular weight and hydrophilicity. Lower-molecular-weight (MW) anthocyanins from elderberry (449–581 Da) were more permeable within the skin in both ex vivo and in vivo models (Kp = 2.3–2.4 × 10−4 cm h−1) than the larger anthocyanins (933-1019 Da) from red radish (Kp = 2.0–2.1 × 10−4 cm h−1). Elderberry and red radish anthocyanins were found at all levels of the stratum corneum and at depths for activity as bioactive ingredients for skin health.