Phlorofucofuroeckol-A (PFF-A) is a phlorotannin extracted from various brown algae. PFF-A shows low toxicity when ingested and various biochemical effects, including antioxidant, anti-inflammatory, anti-cancer, and anti-allergy properties. In this study, various di-O-substituted PFF-A derivatives were synthesized by introducing alkyl or acyl groups at two specific hydroxyls out of the nine nearly equivalent phenolic OH groups present in PFF-A. The exact molecular structures of the synthesized derivatives were analyzed using two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy, which confirmed that the substituents were regioselectively introduced at the 1 OH and 6 OH positions. Small amounts of three mono-O-substituted derivatives were generated as by-products in this reaction, and their structures and regioselectivity were determined using 2D NMR spectroscopy. This study can provide insights into understanding the mechanism of action of eckol-based compounds and developing new drug candidates.