The extraction of xylanase was performed using an aqueous two-phase system (ATPS) based on polyethylene glycol (PEG1540) and various salts. Preliminary studies in a batch extractor showed that the highest extraction efficiency, E = 79.63 ± 5.21%, and purification factor, PF = 1.26 ± 0.25, were obtained with sodium citrate dihydrate-H2O-PEG1540-based ATPS for an extraction time of 10 min. The process was optimized using the experimental Box-Behnken design at three levels with three factors: extraction time (t), xylanase concentration (γ), and mass fraction of PEG in the ATPS (wPEG). Under optimal process conditions (γ = 0.3 mg/mL, wPEG = 0.21 w/w, and t = 15 min), E = 99.13 ± 1.20% and PF = 6.49 ± 0.05 were achieved. In order to intensify the process, the extraction was performed continuously in microextractors at optimal process conditions. The influence of residence time, different feeding strategies, and channel diameter on extraction efficiency and purification factor was further examined. Similar results were obtained in the microextractor for a residence time of τ = 1.03 min (E = 99.59 ± 1.22% and PF = 6.61 ± 0.07) as in the experiment carried out under optimal conditions in the batch extractor. In addition, a batch extractor and a continuous microextractor were used for the extraction of raw xylanase produced by Thermomyces lanuginosus on solid supports.