Fast, selective, and sensitive ultra-high performance liquid chromatography method with tandem mass spectrometry detection for the determination of quercetin and its metabolites with various physico-chemical properties such as molecular weight, lipophilicity, and acid-base properties has been developed. These compounds included small hydrophilic phenolic acids and more lipophilic metabolites with preserved flavonoid structure in small amount of rat plasma. The developed method enables selective separation of phenolic acids and a pair of isomers tamarixetin and isorhamnetin with satisfactory peak shapes and a high sensitivity using mass spectrometry detection. In addition, two sample preparation procedures including protein precipitation and microextraction in packed sorbent (MEPS) were optimized. The sample acidification included in protein precipitation as well as optimizing of MEPS sorbents and elution solvents improved isolation of quercetin and related compounds from rat plasma. Finally, both methods developed for sample preparation were fully validated to demonstrate sufficient accuracy and precision and acceptable matrix effects. Both sample preparation approaches combined with mass spectrometry-based quantification allowed the simultaneous determination of quercetin and its metabolites from a small amount of biological samples of only 50 μL. Due to the fast and non-selective parallel sample preparation, the protein precipitation was eventually applied to plasma samples derived from pharmacokinetic studies.