This study addresses thermal and air permeation properties of a new toughened prepreg system. Voids in the uncured prepreg structure can affect the void content in the final composite structure. A new, toughened prepreg system, commercially available for aircraft structural application, was utilized in this study. The prepreg was subjected to thermal and rheological characterization to understand the basic prepreg properties. These experiments were followed by a prepreg air permeation study to investigate prepreg processing and its influence on the prepreg structure. Crosslinking of the resin matrix was monitored with prepreg specimens without extracting resin from the prepreg. Along with thermal property measurements, the air flow rate significantly decreased in initial static experiments, followed by equilibrium permeability values. An air permeation model divided the air permeability into intralaminar and interlaminar permeabilities. Interlaminar air permeation was found to be more pronounced than intralaminar air permeation in this particular prepreg system. These permeation measurement results were explained using optical microscopy, proving that the application of vacuum could eliminate significant porosity in the laminate. Collectively, understanding prepreg thermal and air permeation properties was considered to be important; the voids in uncured prepreg may cause the voids in the final composite structure. Voids in the prepreg can be attributed to the heterogeneity and anisotropy of the toughened prepreg structure, resulting from particular prepreg processing techniques.