Magnetic resonance imaging (MRI) requires patient immobility and children generally need to be sedated. The ideal sedative agent for functional MRI (fMRI) should only minimally hamper the neurophysiologic effect of the administered sensorial stimulation. This study compares the effect of propofol and midazolam on the fMRI auditory activation pattern in children. Fourteen children in the 3 to 7 year age group without neurologic or auditory deficits were randomly assigned to receive propofol or midazolam for sedation during auditory fMRI. Two patients in the midazolam group were excluded due to positive baseline MRIs. The children were stimulated using a passive listening task. The fMRI signal was modeled using various functions (hemodynamic response function, temporal derivative, and dispersion derivative) to check for the differing temporal characteristics of the signal between the groups. Patients in the propofol group showed activation only in the primary auditory cortex and exhibited a pattern more similar to that of nonsedated adults. Patients in the midazolam group exhibited a more complex pattern, presenting activation areas other than the primary auditory cortex; a delay in the functional response and higher duration variability were also observed. Our sample sizes are too small to derive a conclusive inference. Our preliminary study encourages the hypothesis that propofol is preferable to midazolam to maintain sedation in 3 to 7-year-old children during auditory fMRI because it facilitates the elicitation of a more focused auditory cortical activation pattern with less temporal and spatial dispersion.