Abstract: Anchovies are key forage species in coastal and pelagic food webs, playing crucial ecological and commercial roles in marine ecosystems. Encrasicholina punctifer is a commercially and ecologically important species for which little is known about its osteological development characteristics. Understanding these ontogenetic patterns is essential for explaining phylogenetic relationships within Clupeiformes, informing larval identification in ichthyoplankton surveys, and enhancing aquaculture practices. This study describes the ontogenetic characteristics of the appendicular and median skeletons and fin supports in E. punctifer larvae and juveniles, providing quantitative ontogenetic timelines to address gaps in engraulid developmental biology and contribute to teleost ontogeny research. Larval and juvenile specimens of E. punctifer; size range: 3.00–34.56 mm standard length, SL and notochord length, NL collected from the Philippine Sea were processed using standard Alizarin red and Alcian blue clearing-and-staining technique to differentiate ossified and cartilaginous elements. Specimens were examined under a stereo microscope and imaged with an HTC1600ISP digital camera for detailed morphological analysis of skeletal structures. Caudal complex development was evident by 5.55 mm NL, with the initial appearance of cartilaginous hypurals 1–2 and parhypural, followed by Hy3–5 at 6.08 mm NL. Cartilaginous Hy6 was visible by 9.58 mm SL in postflexion larvae. Six hypural bones were present from the postflexion to juvenile stage. Principal fin rays formed via intramembranous ossification at 6.32 mm NL, and segmentation was evident by 10.24 mm SL. Neural arch 1 appeared at 7.38 mm NL, preceding full haemal arch development. Uroneurals 1–2 and ural centra ossified by 9.58 mm SL, with Hy5 detached from U1 at 10.24 mm SL. Preural centra ossified before the arches. Epurals 1 and 2 were evident by 10.24 mm SL. Dorsal fin proximal radials developed anteriorly and distal radials posteriorly. Pectoral fin development initiated with an ossified cleithrum and the coracoscapular cartilage at 5.25 mm NL. By 10.24 mm SL, cartilaginous neural and haemal arches and spines were distinct. Uroneural 1 initially develops as cartilage. The formation of a pleurostyle aligns with clupeoid fish skeletal ontogeny. Dorsal and anal fin development follows a distinctive pattern, with variability in fin support development. Our results revealed accelerated caudal complex formation in E. punctifer and add new knowledge into the osteological characteristics of the genus Encrasicholina, and aid in understanding larval and juvenile ontogeny of marine teleosts.