Quercetin (Qur) and its major in vivo bioactive metabolites i. e., 3'--methyl quercetin, 4'--methyl quercetin and quercetin 7---D-glucuronide, may be used to treat cerebral ischemia however the poor aqueous solubility and less intestinal absorption of Qur results low bioavailability. To improve Qur bioavailability through preparation of nanoformulation and to develop and validate a sensitive quantification method for Qur detection in brain homogenate. Qur-containing self-nanoemulsifying drug delivery system (Qur-SNEDDS) was developed to form oil-in-water nanoemulsions in situ. Ultra-high performance liquid chromatography electrospray ionization-synapt mass spectrometric method (UHPLC/ESI-QTOF-MS/MS) was developed and validated for quantification whereas for optimal recovery of analyte, a liquid-liquid extraction method (LLE) was used. A droplet size of 94.63±3.17 nm and zeta potential of -17.91±1.02 mV for nanoemuslion, elution time for Qur and internal standard (IS) Rutin as 1.21 and 1.50 min alongwith a transition at m/z 301.04/151.03 and 609.21/299.21, were observed respectively. Similarly, linear dynamic range (1.00 ng/mL-2 000.0 ng/mL), intra and inter-assay i. e., %CV of 0.26-2.04, lower limit of detection (LOD) 0.08 ng/mL as well as lower limit of quantitation (LOQ) as 0.131 ng/mL were also observed. The developed method have advantage over previous all methods i. e., less time consuming (<3.0), low consumption of solvents (flow rate 0.20 mL/min.) via small size column, more accuracy and specificity as well as use of acetonitrile as compared to hazardous solvents. This certainly adds advantages for green chromatography technique and supports application of current developed method for quantification and evaluation of Qur-SNEDDS.