Anthocyanins are known for their therapeutic efficacy for many human diseases, including cancer. After ingestion, anthocyanins degrade due to oxidation and enzymatic breakdown, resulting in reduced therapeutic efficacy. Direct delivery to target tissues and entrapment of anthocyanins increases their stability, bioavailability, and therapeutic efficacy. The objective of the present study was to develop a direct delivery system of anthocyanins into pulmonary tissues via encapsulated nanocarriers. A cyanidin-3-O-glucoside (C3G)-rich anthocyanin extract was prepared from well-ripened haskap (Lonicera caerulea L.) berries (HB) and encapsulated in three different polymeric nanocarrier systems: polyethylene glycol-poly(lactide-co-glycolide), maltodextrin, and carboxymethyl chitosan (CMC). The anthocyanin encapsulation efficiency was significantly higher in CMC (10%) than in the other two polymers. The cytotoxicity and cytoprotective effect of HB anthocyanin-encapsulated CMC (HB-CMC, 4 μg of C3G equivalent anthocyanin in 2 mg/mL nanoparticle) and anthocyanin-free CMC (E-CMC, 2 mg/mL) were tested for cytotoxicity using human normal lung epithelial BEAS-2B cells. The CMC nanoparticles were not cytotoxic for BEAS-2B cells. The HB-CMC nanoparticles reduced carcinogen-induced oxidative stress in BEAS-2B cells and restored the expression of superoxide dismutase and glutathione peroxidase enzymes. The HB-CMC nanoparticles also reduced carcinogen-induced DNA single-strand breaks and alkaline-labile sites but not the double-strand breaks. The E-CMC, HB-CMC (28 μg C3G equivalent/mouse/day for six days), or the same dose of free HB anthocyanin was administered to A/JCr mice through a nose-only passive inhalation device. C3G and its metabolites, cyanidin, peonidin-3-O-glucoside, and cyanidin-3-O-glucuronide, were detected by UPLC/ESI/Q-TOF-MS in the lungs of mice after one hour of exposure. Therefore, the CMC could be a promising noncytotoxic candidate to encapsulate HB anthocyanin. Direct delivery of anthocyanin to lung tissues enhances tissue retention, slows phase 2 metabolism, and improves therapeutic efficacy.