A new magnetic molecularly imprinted polymer (MMIP) was firstly synthesized using terephthalic acid as a functional monomer to extract atenolol (ATL) from human plasma by magnetic solid phase extraction (MSPE). ATL enantiomers separation was performed by capillary electrophoresis using carboxymethyl-β-cyclodextrin (CM-β-CD: 5.5 mg) as chiral selector in background electrolyte with 125 mmol L−1 triethylamine pH 6.0 using a capillary with 75 µm of internal diameter. After MSPE optimization, the best conditions were: 500 µL of ultrapure water as washing solvent, 1000 µL of methanol as eluting solvent, 25 mg of MMIP, and 250 µL of sample (human plasma at pH 12.5). Recoveries/relative standard deviation percentage were 75.8 ± 6.3% and 76.1 ± 5.7% for (-)-(S)-ATL and (+)-(R)-ATL, respectively. The method was linear over the concentration range from 5.0 to 1500.0 ng mL−1, with coefficients of correlation larger than 0.99 for both enantiomers. The method was successfully applied in plasma samples from volunteers under continuous use of ATL racemate. Finally, MMIP imprinting test confirmed that the material was selective for ATL, with low recoveries for other drugs.