A scheme for achieving accurate, quantitative analysis of fluid inclusions by synchrotron radiation X-ray fluorescence (SXRF) spectroscopy is proposed. Equations accounting for the inclusion depth and thickness are derived and verified through analysis of Cu and Zn in synthetic fluid inclusions. The method involves the construction of a two-dimensional distribution map of XRF for each element (Cu and Zn), followed by the measurement of XRF over a longer irradiation period to obtain a value of “relative intensity”. The relative intensity is shown to be more accurate than the integrated intensity obtained for the entire inclusion area in the map. The equations derived for inclusion fluid concentrations in terms of the relative intensity produce results that are consistent with the values expected by calculation using the mass absorption coefficients and density of quartz. The proposed scheme is also applicable for the analysis of other elements with similar atomic number in a range of host minerals.