Investigating the functional modular organisation of the brain provides a deeper insight into the complex network phenomena that govern cognitive processes like olfactory perception. In recent years, understanding the neural mechanisms associated with this unique sensory modality has been gaining traction, due to increasing applications in various clinical and non-clinical research areas. Anatomically distinct, but functionally interconnected brain regions, organized as communities (or functional modules) enable high-order cognitive processes by providing support for the integration of several localized, highly specialized processing functions. In this work, to understand the elicited neuronal communication pathways in response to fragrance stimuli of varying positive valence, graph theoretical network metrics were calculated to quantify differences in brain’s functional networks modular organization estimated from source localised EEG signals. We found that inter-modular connectivity differences in neural responses to olfactory stimuli of different pleasantness levels may be linked to inhibitory processes in the frontal and central-occipital regions. Moreover, our results indicate that significant intra-modular connectivity changes may be linked to emotional processing of fragrance stimuli of varying pleasantness.