Lemon fragrance is known for its stimulating properties, but its mechanisms of action are not well known yet. This study aimed to examine the effect of lemon essential oil inhalation on healthy participants’ alertness level and their neural correlates using magnetic resonance imaging (MRI). Twenty-one healthy men underwent functional MRI scans in different conditions: a resting state condition, a condition where they were exposed to passive lemon smelling (alternating exposure to lemon and breathing fresh air), and a control condition without lemon fragrance diffusion –the order of the last two conditions being randomized. Alertness levels were assessed immediately after each condition using the Karolinska Sleepiness Scale. Voxel-wise whole-brain global functional connectivity and graph theory analyses were computed to investigate brain functional connectivity and network topology alterations. After lemon fragrance inhalation, we observed a higher level of alertness as compared to resting state –but not compared to control condition. During lemon fragrance inhalation, we found increased global functional connectivity in the thalamus, paralleled by decreased global connectivity in several cortical regions such as precuneus, postcentral and precentral gyrus, lateral occipital cortex and paracingulate gyrus. Graph theory analysis revealed increased network integration in cortical regions typically involved in olfaction and emotion processing such as olfactory bulb, hypothalamus and thalamus, while decreased network segregation in several regions of the posterior part of the brain during olfaction as compared to resting state. The present findings suggest that lemon essential oil inhalation could increase the level of alertness.