The current study aimed to evaluate the cytotoxic potential of the total extract of the soft coral Nephthea sp. and its derived fractions (petroleum ether, ethyl acetate, n-butanol and acetone) in addition to their green synthesized silver nanoparticles (AgNPs) against hepatocellular carcinoma (HepG2) and colon adenocarcinoma (HT29) cell lines. Of these, the petroleum ether fraction exhibited potent inhibitory activity against HepG2 cells, with an IC50 value of 1.10 ± 0.03 μg/ml, while the n-butanol fraction revealed significant cytotoxic potential against HT29 cells (IC50= 3.69 ± 0.16 μg/ml). On the other hand, the prepared AgNPs of both the total extract and its ethyl acetate fraction demonstrated the maximum inhibitory effects towards HepG2 and HT29 tumor cells, respectively (IC50= 0.35 ± 0.01 and 8.97 ± 0.48 μg/ml, respectively). Moreover, an in-silico molecular docking analysis of a group of 14 identified metabolites from the petroleum ether fraction showed the considerable binding affinity of compounds 1 (nephthoside monoacetate), 5 (chabrolobenzoquinone E), 10 (chabrolohydroxybenzoquinone E), and 12 (2-N-nonanoyl-4,5-dihydrosphingosine) to the common tyrosine kinase, epidermal growth factor receptor (EGFR), which might suggest their contribution to the observed cytotoxic potential of this fraction of Nephthea sp. These results could therefore pave the way towards further search for varied antitumor candidate metabolites from Nephthea sp.