Continuous fluidic sampling systems allow collection of brain biomarkers in vivo. Here, we propose a new sampling paradigm, Droplet on Demand (DoD), implemented in a microfabricated neural probe. It allows sampling droplets loaded with molecules from the brain extracellular fluid punctually, without the long transient equilibration periods typical of continuous methods. It uses an accurate fluidic sequence and correct operation is verified by the embedded electrodes. As a proof of concept, we demonstrated the application of this novel approach in vitro and in vivo, to collect glucose in the brain of mice, with a temporal resolution of 1-2 minutes and without transient regime. Absolute quantification of the glucose level in the samples was performed by direct infusion nanoelectrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS). By adjusting the diffusion time and the perfusion volume of DoD, the fraction of molecules recovered in the samples can be tuned to mirror the tissue concentration at accurate points in time. This makes quantification of biomarkers in the brain possible within acute experiments of only 20 to 120 minutes. DoD provides a complementary tool to continuous microdialysis and push-pull sampling probes. The advances allowed by DoD will benefit quantitative molecular studies in the brain, namely for molecules involved in volume transmission or for protein aggregates that form in neurodegenerative diseases over long periods.