We describe a near-infrared-sensitive molecular imaging probe based on hydrogel complexes that can target a stem-like gastric cancer cell marker (CD44, a marker that often correlates with a poor prognosis in patients). Thus, CD44-targetable and near-infrared-sensitive supramolecular hydrogels (NIRSHs, Cy5.5-conjugated polyethyleneimine/hyaluronic acid polyplexes) were fabricated by polyplexing in an aqueous medium. NIRSHs demonstrated good water-stability, biocompatibility, and specificity to CD44-expressing stem-like gastric cancer cells. Furthermore, NIR-sensitive in vivo imaging potentials of CD44-targetable NIRSHs for heterotopic/orthotopic xenograft mouse models were investigated.