The Eocene–Miocene carbonate deposition in the Gulf of Papua (GoP) corresponds to the carbonate evolution phase of this continental margin mixed depositional system. Global sea-level (eustatic) fluctuations appear to have been the most important factor influencing the mixed depositional system development during its carbonate phase. Development of the major carbonate system in the Gulf was initiated during the Eocene. Subsequent to an early Oligocene hiatus, the carbonate system expanded its surface area, vertically aggraded, then systematically backstepped, and finally partially drowned during the late Oligocene–early part of the early Miocene. During the late early Miocene–early middle Miocene, the carbonate system continued its vertical growth in most platform areas, where it was able to keep up with sea-level rise. At the early middle/late middle Miocene (Langhian/Serravallian) boundary, carbonate deposition shifted downward during a long-term sea-level regression, exposing most of the early middle Miocene platform tops. Following this downward shift, active carbonate production became restricted during the late middle Miocene to only the northeastern part of the study area, and carbonate accumulation was characterized by four systematically prograding units. At the very beginning of the late Miocene, the platform tops were re-flooded. The carbonate system was partially drowned, systematically backstepped, and locally aggraded during part of the late Miocene, the early Pliocene, and the Quaternary. The overall organization of the carbonate sequence geometries, observed in the GoP, display a clear pattern, often referred to as the Oligocene–Neogene stratigraphic signature. This pattern is identical to contemporaneous sedimentary patterns observed in pure carbonate systems such as in the Maldives and in the Bahamas, and also in some siliciclastic systems. Because this pattern is observed in several globally distributed locations, the recognition of the Oligocene–Neogene stratigraphic signature in the GoP demonstrates that the depositional evolution during the late Oligocene–Miocene and the early Pliocene must have been dominantly controlled by eustatic fluctuations.