Early childhood caries (ECC) involve extensive coronal tooth structure loss, and tooth reconstruction remains highly challenging. To fulfill preclinical assessment, the present study investigated the biomechanics of non-restorable crownless primary molars that were restored by stainless steel crowns (SSC) using different composite core build-up materials. Computer-aided design-integrated 3D finite element and modified Goodman fatigue analyses were performed to determine stress distribution, risk of failure, fatigue life and dentine–material interfacial strength for the restored crownless primary molars. A dual-cured resin composite (MultiCore Flow), a light-cured bulk-fill resin composite (Filtek Bulk Fill posterior), a resin-modified glass-ionomer cement (Fuji II LC) and a nano-filled resin-modified glass-ionomer cement (NRMGIC; Ketac N100) were used as core build-up composite materials in the simulated models. The finite element analysis showed that types of core build-up materials affected the maximum von Mises stress only in the core materials (p-value = 0.0339). NRMGIC demonstrated the lowest von Mises stresses and revealed the highest minimum safety factor. The weakest sites were along the central grooves regardless of type of material, and the ratio of shear bond strength to maximum shear stress at the core–dentine interface of the NRMGIC group was lowest among the tested composite cores. However, all groups provided lifetime longevity from the fatigue analysis. In conclusion, core build-up materials differentially influenced the von Mises stress (magnitude and distribution) and the safety factor in crownless primary molars restored with core-supported SSC. However, all materials and the remaining dentine of crownless primary molars provided lifetime longevity. The reconstruction by core-supported SSC, as an alternative to tooth extraction, may successfully restore non-restorable crownless primary molars without unfavorable failures throughout their lifespan. Further clinical studies are required to evaluate the clinical performance and suitability of this proposed method.