This paper reports a novel method for the rapid determination of vitamin B12 concentration in a continuous-flow lab-on-a-chip system. This new method is based on luminol-peroxide chemiluminescence (CL) assays for the detection of cobalt(II) ions in vitamin B12 molecules. The lab-on-a-chip device consisted of two passive micromixers acting as microreactors and a double spiral microchannel network serving as an optical detection region. This system could operate in two modes. In the first mode, samples are acidified and evaluated directly in the microchip. In the second mode, samples are treated externally by acidification prior to detection in the microchip. In the first mode, the linear range obtained was between 1.00 ng ml−1 to 10 μg ml−1, R2 = 0.996, with a relative standard deviation (RSD) of 1.23 to 2.31% (n = 5) and a limit of detection (lod) of 0.368 pg ml−1. The minimum sample volume required and the analytical time were 30 μl and 3.6 s, respectively. In the second mode, the linear range obtained was between 0.10 ng ml−1 to 10 μg ml−1, R2 = 0.994, with the RSD of 0.90 to 2.32% (n = 6) and a lod of 0.576 pg ml−1. The minimum sample and the analytical time required were 50 μl and 6 s, respectively. The lab on a chip working in mode II was successfully used for the determination of vitamin B12 concentrations in nutritional supplemental tablets and hen egg yolks.