The beneficial health properties of organic acids make them target compounds in multiple studies. This is the reason why developing a simple and sensitive determination and investigation method of organic acids is a priority. In this study, an effective method has been established for the determination of organic (lactic, glycolic, and malic) acids in saffron stigmas. N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide (MTBSTFA) was used as a derivatization reagent in gas chromatography combined with mass spectrometric detection (GC/MS). The saffron stigmas extract was evaporated to dryness with a stream of nitrogen gas. The derivatization procedure: 0.1 g of dried extract was diluted into 0.1 mL of tetrahydrofuran, then 0.1 mL MTBSTFA was orderly and successively added into a vial. Two different techniques were used to obtain the highest amount of organic acid derivatives from saffron stigmas. To the best of our knowledge, this is the first report of the quantitative and qualitative GC/MS detection of organic acids in saffron stigmas using MTBSTFA reagent, also comparing different derivatization conditions, such as time, temperature and the effect of reagent amount on derivatization process. The identification of these derivatives was performed via GC-electron impact ionization mass spectrometry in positive-ion detection mode. Under optimal conditions, excellent linearity for all organic acids was obtained with determination coefficients of R2 > 0.9955. The detection limits (LODs) and quantitation limits (LOQs) ranged from 0.317 to 0.410 µg/mL and 0.085 to 1.53 µg/mL, respectively. The results showed that the highest yield of organic acids was conducted by using 0.1 mL of MTBSTFA and derivatization method with a conventional heating process at 130 °C for 90 min. This method has been successfully applied to the quantitative analysis of organic acids in saffron stigmas.