We present new biostratigraphic analyses of approximately 200 outcrop samples and review biostratigraphic data from 136 public domain exploration wells across western New Guinea. Biostratigraphic ages and palaeodepositional environments were interpreted from occurrences of planktonic and larger benthic foraminifera, together with other fossils and environmental indicators where possible. These data were compared with existing geological maps and exploration well data to reconstruct the palaeogeography of western New Guinea from the Carboniferous to present day. In addition, we used the known bathyal preferences of fossils to generate a regional sea-level curve and compared this with global records of sea-level change over the same period. Our analyses of the biostratigraphic data identified two major transgressive-regressive cycles in regional relative sea-level, with the highest sea levels recorded during the Late Cretaceous and Late Miocene and terrestrial deposition prevalent across much of western New Guinea during the Late Paleozoic and Early Mesozoic. An increase in the abundance of carinate planktonic foraminifera indicates a subsequent phase of relative sea-level rise during a regional transgressive event between the Late Jurassic and Late Cretaceous. However, sea-levels dropped once more during a regressive event between the Late Cretaceous and the Paleogene. This resulted in widespread shallow water carbonate platform development in the Middle to Late Eocene. A minor transgressive event occurred during the Oligocene, but this ceased in the Early Miocene, likely due to the collision of the Australian continent with intra-Pacific island arcs. This Miocene collision event resulted in widespread uplift that is marked by a regional unconformity. Carbonate deposition continued in platforms that developed in shallow marine settings until these were drowned during another transgressive event in the Middle Miocene. This transgression reached its peak in the Late Miocene and was followed by a further regression culminating in the present day topographic expression of western New Guinea.