Loss of function mutations in the TRAPPC9 gene causes autosomal recessive intellectual disability and microcephaly. A mouse model was generated to investigate the effects of TRAPPC9 knockout in mice. In vivo and ex vivo MRI were used alongside behavioural tests to probe differences in brain volume and learning ability. In vivo MRI demonstrated significant differences between the whole brain, cerebellar and corpus callosum volumes of adult TRAPPC9 knockout mice and wildtype controls. Behavioural assays also revealed significant differences in learning ability. These results align with the human condition and suggest the model is appropriate for further study of TRAPPC9 knockout.