The currently favored hypothesis for Late Paleozoic Ice Age glaciations is that multiple ice centers were distributed across Gondwana and that these ice centers grew and shank asynchronously. Recent work has suggested that the Transantarctic Basin has glaciogenic deposits and erosional features from two different ice centers, one centered on the Antarctic Craton and another located over Marie Byrd Land. To work towards an understanding of LPIA glaciation that can be tied to global trends, these successions must be understood on a local level before they can be correlated to basinal, regional, or global patterns. This study evaluates the sedimentology, stratigraphy, and flow directions of the glaciogenic, Asselian–Sakmarian (Early Permian) Pagoda Formation from four localities in the Shackleton Glacier region of the Transantarctic Basin to characterize Late Paleozoic Ice Age glaciation in a South Polar, basin-marginal setting. These analyses show that the massive, sandy, clast-poor diamictites of the Pagoda Fm were deposited in a basin-marginal subaqueous setting through a variety of glaciogenic and glacially influenced mechanisms in a depositional environment with depths below normal wave base. Current-transported sands and stratified diamictites that occur at the top of the Pagoda Fm were deposited as part of grounding-line fan systems. Up to at least 100 m of topographic relief on the erosional surface underlying the Pagoda Fm strongly influenced the thickness and transport directions in the Pagoda Fm. Uniform subglacial striae orientations across 100 m of paleotopographic relief suggest that the glacier was significantly thick to “overtop” the paleotopography in the Shackleton Glacier region. This pattern suggests that the glacier was likely not alpine, but rather an ice cap or ice sheet. The greater part of the Pagoda Fm in the Shackleton Glacier region was deposited during a single retreat phase. This retreat phase is represented by a single glacial depositional sequence that is characteristic of a glacier with a temperate or mild subpolar thermal regime and significant meltwater discharge. The position of the glacier margin likely experienced minor fluctuations (readvances) during this retreat. Though the sediment in the Shackleton Glacier region was deposited during a single glacier retreat phase, evidence from this study does not preclude earlier or later glacier advance–retreat cycles preserved elsewhere in the basin. Ice flow directions indicate that the glacier responsible for this sedimentation was likely flowing off of an upland on the side of the Transantarctic Basin closer to the Panthalassan–Gondwanide margin (Marie Byrd Land), which supports the hypothesis that two different ice centers contributed glaciogenic sediments to the Transantarctic Basin. Together, these observations and interpretations provide a detailed local description of Asselian–Sakmarian glaciation in a South Polar setting that can be used to understand larger-scale patterns of regional and global climate change during the Late Paleozoic Ice Age.