Comprehensive field, litho-, biostratigraphy, and paleoenvironmental studies of the upper Paleocene–lower Eocene (P–E) boundary interval in the Gabal El-Gir area were conducted. Two selected sections El-Gir-1 and El-Gir-2 were investigated. The prevailed paleoenvironmental conditions were discussed in the frame of the nannofossils, planktonic, and benthic foraminiferal assemblages. Benthic foraminifera assemblages indicate a remarkable turnover across the PETM. The extinction of Angulogavelinella avnimelechi at the base of the PETM represents a significant marker for the base of the benthic foraminifera extinction event at this site and other neritic sites in the Tethyan region. The dominance of calcareous planktonic excursion taxa at the base of the PETM indicates adaptation to extremely warm sea surface temperatures and low nutrient levels. Also, our data suggests that the biotic responses to environmental change in the early Eocene resembled those observed in the early Eocene hyperthermals at the Dababiya and El-Ballas sections. This could indicate that similar processes characterized the Egyptian sedimentary basin during the early Eocene. Stratigraphically, despite the limited distance between the studied sections, the Dababiya Quarry Member (DQM) in El-Gir-1 resemble those of the Global Stratotype Section and Point (GSSP) but reduced in thickness. While in El-Gir-2, the lower part of the DQM was missing. These findings could indicate that the DQM was deposited in a submarine channel. Three third-order depositional sequences were recognized covering the P–E interval. The reconstructed sea level curve shows the presence of eustatic similarities with the global sea level.