The main aim of this study was to confirm the relationship between executive performance and salivary alpha-amylase (SAA) activity in a sample of 64 healthy children (39 boys), and compare it to the association of SAA output and salivary flow rate (SFR). Executive functioning was assessed via fluency, trail-making, rings and inhibition tasks from the Batería de Evaluación Neuropsicológica de la Función Ejecutiva en Niños [Battery of Neuropsychological Assessment for Executive Function in Children] (ENFEN), merged into an ENFEN total score. SAA activity, output, and SFR were measured at baseline, one minute before, and one minute after the end of a neuropsychological testing session. Our results confirmed a direct, linear and significant association between SAA activity and executive functioning, r(64) = .351, p < .05, and extended it to SAA output, r(64) =.431, p < .05. The mean level of SAA output was the best predictor of executive functioning (β = .431, p < .05) and explained 18.2 % of the variance in ENFEN total score. In sum, and compared to SAA activity, measuring SAA output may be a more precise and indirect marker to assess executive functioning in children.