The temporal specificity of functional magnetic resonance imaging (fMRI) is limited by a sluggish and locally variable hemodynamic response trailing the neural activity by seconds. Here, we demonstrate for an attention capture paradigm that it is, never the less, possible to extract information about the relative timing of regional brain activity during cognitive processes on the scale of 100 ms by comparing alternative signal models representing early versus late activation. We demonstrate that model selection is not driven by confounding regional differences in hemodynamic delay. We show, including replication, that the activity in the dorsal anterior insula is an early signal predictive of behavioral performance, while amygdala and ventral anterior insula signals are not. This specific finding provides new insights into how the brain assigns salience to stimuli and emphasizes the role of the dorsal anterior insula in this context. The general analytic approach, named “Cognitive Timing through Model Comparison” (CTMC), offers an exciting and novel method to identify functional brain subunits and their causal interactions.