Fe3O4 magnetic nano-particles functionalized by sodium dodecyl sulphate (SDS) were used for separation and efficient removal of Brilliant Green (BG) dye from aqueous solutions in a batch system. Adsorption process of dye was optimized by means of a multivariate approach, such as response surface methodology. Box–Behnken design was performed to evaluate the influences of various experimental factors for instance: pH, adsorbent dose (m) and initial dye concentration (Cd), on the removal percent (R%) and uptake capacity (q). The optimum conditions for BG adsorption by nano-Fe3O4–SDS were found to be: pH = 4; nano-Fe3O4 = 8 mg; SDS = 10.8 mg and Cd = 600 mg /L. Simultaneous optimization of both responses R% and uptake capacity (q) was also performed through applying a desirability function approach. The results obtained for simultaneous optimization of R% = 64 and q = 440 mg/g with 99% overall desirability (D = 0.99) are: pH = 4; Cd = 600 mg/L; nano-Fe3O4 = 8.8 mg and SDS = 10.9 mg. Under optimum conditions, pre-concentration of water sample was achieved by containing BG with the enrichment factor of 63 and DL = 3.0 μg/L and RSD = 2.1% (n = 9) for 21.14 μg/L. Isotherm modelling and thermodynamic studies for further information about BG behaviour with nano-Fe3O4–SDS adsorbent were investigated. The morphology and properties of the magnetite nano-particles produced was determined by scanning electron microscopy, X-ray diffraction, vibrating sample magnetometer, Fourier transform infrared spectroscopy and thermogravimetric analysis. As a result of this study, functionalizing Fe3O4 magnetic nano-particles considerably improved the efficiency of the adsorption process of BG.