A new approach for the implementation of liquid-liquid extraction in a sequential injection manifold is presented. The manifold consists of two syringe pumps and one multi-position valve. The use of a 30% MeOH/H2O (v/v) solution as the carrier, with isobutanol as the extractant, made it possible to avoid the problems associated with the different affinities of the organic and aqueous phases for Teflon tubing, and the formation of bubbles. The suitability of the proposed method was demonstrated by the determination of thiamine in pharmaceutical preparations and dietary supplements. Detection and quantification limits were estimated as 9 and 30μgL(-1), respectively. The repeatability was lower than 3% and the intermediate precision (3d) was lower than 7%. The sample throughput was 14 samples per h. The results were in agreement with a high-performance liquid chromatography-electrospray/mass spectrometry reference method.