The phytochemical investigation of the methanol extracts of the leaves and twigs of Mitrephora tomentosa Hook. f. & Thomson resulted in the isolation and identification of undescribed polyacetylenic ester-neolignan derivatives, along with six known compounds. These six undescribed natural products were named as mitrephentosins A-F. The structures of these compounds were determined by spectroscopic techniques including UV, IR, NMR, and mass spectrometric analyses. The absolute configurations of mitrephentosins A-F were determined based on specific rotations values and ECD spectral data by comparisons made with the known parent neoligan compound mitredrusin. Mitrephentosins C, E, and F showed moderate antimalarial activities (IC50 values of 13.3–24.6 μM) against the Plasmodium falciparum strains TM4/8.2 and K1CB1 and were not toxic to Vero cells, while the other isolated compounds were not active against these P. falciparum strains.