A semi-automated microextraction by packed sorbent (MEPS) method was developed for the HPLC determination of ellagic acid (EA) in juice samples. The procedure includes enrichment of the analyte on a nanoporous silica sorbent by the MEPS method using a laboratory-made programmable apparatus. Three functionalized SBA-15 nanoporous sorbents were evaluated for this purpose and 3-[bis(2-hydroxyethyl)amino]propyl-triethoxysilane (HPTES)-SBA-15 showed superior efficiency. Only 2 mg of the adsorbent packed in a syringe’s hub was sufficient for a quantitative recovery of EA. Different factors influencing the performance of the MEPS method such as the nature of desorption solvent, elution volume, pH, number of extraction cycles (draw–eject) and sample volume were carefully studied and optimized. Under the optimized conditions, a detection limit of 0.8 mg/L and a linear calibration curve with an R2 of 0.9995 were obtained for EA. The average recovery of the analyte for juice samples was 97.6% with a relative standard deviation of 4.4% for six replicates. The method was successfully applied to the HPLC determination of EA in pomegranate and grape juice samples.