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This study theoretically examines a partially perforated caisson sitting on a rubble mound foundation. A Jarlan-type perforated caisson consisted of a perforated front wall, a solid rear wall and a wave-absorbing chamber between them. When the incident wave overlaps with waves reflected from the perforated front wall and the solid rear wall, its energy can be significantly reduced. Correlative research projects primarily focused on fully and partially perforated caissons sitting on a solid seabed or a solid step. The investigation of partially perforated caisson sitting on a rubble-mound foundation was scant and mainly by means of experiments and numerical modeling. In present research, a mathematical model based on eigenfunction expansion method is developed to predict regular and irregular wave reflections from a partially perforated caisson sitting on a rubble-mound foundation. This model has clear physical meaning and is easy to solve. It covers all details from previous research on perforated caissons, and further considers the effect of the permeable rubble mound foundation.