Prostaglandins (PGs) with cytoprotective activity were studied for a long time, and a few PGE1 and PGE2 stable analogues were promoted as drugs: arbaprostil, enprostil, misoprostol, and rioptostol. Similarly, nocloprost, a 9β-chlorine prostaglandin analogue, and many 9β- and 11β-substituted prostaglandins were synthesized and studied for their biological activity. We previously synthesized new 9β-halogenated prostaglandins with an ester group at the carbon atom 6 (PGs numbering) by the reaction of a δ-lactone intermediate with diols in acid catalysis. These compounds were used in the current molecular docking study to determine their potential cytoprotective (anti-ulcer) activity. The current study was done with the CLC Drug Discovery Workbench 2.4. software and an oxidoreductase enzyme receptor, chosen from the Protein Data Bank, ID: 4KEW (www.rcsb.org). We used two recognized drugs, omeprazole (co-crystallized with the enzyme) and nocloprost, as the standard. The 9β-halogenated prostaglandin analogs were docked. Nocloprost and all 9β-halogenated compounds had docking scores greater than that of omeprazole. The majority of the 9β-halogenated analogs had docking scores even greater than that of nocloprost, indicating that these compounds could have potential cytoprotective (anti-ulcer) activity. A few correlations between docking score and substituents on the prostaglandin skeleton were found.