Heterotrigona itama stingless bee propolis extract is known for its diverse bioactive compounds, making it a potential natural shield against UV radiation. This research assesses the photoprotective potential of crude ethanol extract from H. itama propolis collected from four structures (involucrum, pillar, pot, and entrance) of five bee hives (H1-H5), totalling 20 samples. Initially, the samples underwent testing for SPF value and UV absorption spectra. The crude ethanol extract (E) from the involucrum (H4) with the highest SPF value and broadest spectrum was selected for fractionation using hexane and water. Subsequently, the extract (E) and its hexane (H) and water (W) fractions were subjected to SPF analysis, UVA/UVB absorption assessment, determination of total phenolic and flavonoid content, free radical scavenging capacity, anti-collagenase effects, and cytotoxicity assessment. Additionally, LC-MS/MS analysis was performed to identify chemical constituents in the active fraction (W). The extract E demonstrated an SPF of 8.23 ± 0.09 and UV absorption. Notably, its fraction W exhibited the highest SPF (16.55 ± 0.24) at 100 μg/mL, surpassing the H fraction (SPF 5.7 ± 0.45). Phenolic content was highest in the H fraction (388.95 ± 4.54 mg/g GAE DW), followed by the W fraction (286.76 ± 6.48 mg/g GAE DW) and crude E (91.83 ± 4.12 mg/g GAE DW) from the involucrum. Regarding flavonoids, the fraction W led with 79.82 ± 6.21 mg/g QE DW, followed by the H fraction (45.56 ± 0.05 mg/g QE DW) and E (34.57 ± 1.11 mg/g QE DW). The extract E also exhibited modest DPPH scavenging (EC50 = 120 μg/mL), while the H fraction demonstrated stronger activity (EC50 = 4.37 μg/mL), and the W fraction displayed moderate effects (EC50 = 17.55 μg/mL). Notably, the W fraction showed remarkable anti-collagenase activity, outperforming the positive control, EG. HaCaT cell cytotoxicity revealed that the extract E was cytotoxic, whereas the H and W fractions showed no toxicity. LC-MS/MS analysis identified bioactive flavonoids (e.g., pratensein, quercetin) in the W fraction. These findings highlight the superior photoprotective properties of the water fraction from the involucrum of H. itama stingless bee propolis extract, suggesting its potential as a natural and effective ingredient for sunscreen and skincare formulations.