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Aquaplanet experiments are important tools for understanding and improving physical processes simulated by global models; yet, previous aquaplanet experiments largely differ in their representation of subseasonal tropical rainfall variability. This study presents results from aquaplanet experiments produced with the Model for Prediction Across Scales‐Atmosphere (MPAS‐A)—a community model specifically designed to study weather and climate in a common framework. The mean climate and tropical rainfall variability simulated by MPAS‐A with varying horizontal resolution were compared against results from a recent suite of aquaplanet experiments. This comparison shows that, regardless of horizontal resolution, MPAS‐A produces the expected mean climate of an aquaplanet framework with zonally symmetric but meridionally varying sea‐surface temperature. MPAS‐A, however, has a stronger signal of tropical rainfall variability driven by convectively coupled equatorial waves. Sensitivity experiments with different cumulus parameterizations, physics packages, and vertical grids consistently show the presence of those waves, especially equatorial Kelvin waves, in phase with lower‐tropospheric convergence. Other models do not capture such rainfall‐kinematics phasing. These results suggest that simulated tropical rainfall variability depends not only on the cumulus parameterization (as suggested by previous studies) but also on the coupling between physics and dynamics of climate and weather prediction models. Plain Language Summary: Continuous improvements of weather and climate models are necessary to advance both our understanding and ability to predict high‐impact weather under present and future climates. One particular area requiring model improvements is the representation of tropical rainfall variability happening at subseasonal timescales. With this issue in mind, we produced experiments using a simplified version of a global model called an aquaplanet—an Earth‐like water‐covered surface devoid of land, topography, sea‐ice, or seasons. We first demonstrate that the model used in this study, whichwas specifically designed to study weather and climate, simulates a mean climate that is consistent with other aquaplanet experiments. We also demonstrate that the model is able to capture tropical rainfall variability driven by phenomena called convectively coupled Kelvin waves. Because other models do not capture this variability, we show experiments changing various components of the model to explore the influence of those components on the representation of Kelvin waves. Those experiments demonstrate that, contrary to previous perceptions, the component that approximates deep cumulus clouds is not the only responsible component. Instead, the ability to produce a certain phasing between winds and rainfall appears to explain whether a model can capture Kelvin waves. Key Points: Aquaplanet experiments with the Model for Prediction Across Scales‐Atmosphere (MPAS‐A) produce similar mean climate to other global modelsMPAS‐A experiments better capture convectively coupled equatorial waves compared to other models, even when using different cumulus schemesStructural uncertainty between low‐level convergence and rainfall phasing underlies model discrepancies in tropical rainfall variability [ABSTRACT FROM AUTHOR]