An inkjet-printed electrochemical bisphenol A (BPA) sensor was developed by exploiting the high dispersibility of shortened and defect-rich nitrogen-doped multi-walled carbon nanotubes (MWCNTs). To enhance the dispersibility of MWCNTs in water-based dispersant, the defect concentration was increased by both creating shortened CNT and heteroatom doping, and modification of their surfaces with sulfonate (SO3H) groups. CNT-based inks were prepared by dispersing modified CNT structures in deionized water and the stability and physical properties of the inks were determined. The results suggested that the shortening of MWCNT and SO3H functionalization strategies improved the stability of CNT-based aqueous inks significantly, which enabled the preparation of highly concentrated inks up to 20 mg/ml with high stability. The CNT-based inks were printed on flexible polyethylene tetraflate (PET) and used as an electrochemical BPA sensor. The electrochemical analytical performance of the printed sensors was evaluated using chronoamperometry and differential pulse voltammetry methods. The sensors showed a wide linear range of 5–100 (CA) and 60–700 (DPV) with a LOD of 0.7 μM. The real sample analysis was conducted in milk and high recoveries were obtained, suggesting the applicability of the sensors in real media.