In this research, we used the non-SELEX method to successfully select an aptamer that binds to the protein target (bovine catalase) with a KD value in the low micro molar range. The time window was determined for the target and aptamer library by optimizing the buffer conditions using 3 x Tris-glycine-potassium phosphate (TGK) buffer as the run buffer and 1x TGK as the selection buffer to give the biggest complex peak. Fractions were collected by multistep nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM)-based partitioning for three rounds of selection. The fractions from each round were enriched using PCR and the progress of selection was monitored using bulk affinity analysis. Fraction 2 was determined to have the optimal bulk affinity (0.75 mu M) and this enriched library was cloned and sequenced giving four aptamer sequences. These sequences were verified using affinity capillary electrophoresis (CAT 1 0.237 mu M) and fluorescence intensity measurements (CAT 1 0.430 mu M). The specificity of the aptamer was also determined by fluorescence intensity measurements. The results showed that the aptamer with the highest binding affinity showed at least a 100-fold decrease in affinity toward four other proteins (i.e. lysozyme, trypsinogen, chymotrypsinogen A, and myoglobin) tested and this confirmed that the aptamer exhibited a distinct specificity toward bovine catalase. This aptamer will be useful in biosensing, Western blot, and biomarker identification.