Drug-coated balloons (DCBs) are a recent technology developed to treat peripheral artery disease (PAD). Along with a suitable formulation of antiproliferative drug and excipient, coating method is an important aspect of a DCB as these factors affect coating characteristics and drug delivery to the treatment site. The multiple release tailored medical devices DCB (MR-TMD-DCB), designed to achieve multiple inflations to treat complex PAD, contains paclitaxel (PAT) as the antiproliferative drug and polyethylene oxide (PEO) as the excipient. In our previous studies, the MR-TMD-DCB was coated using a manual dip coating method. In this study, an automated micropipette coating method was developed using a modified spray coating instrument to coat the MR-TMD-DCB. First, the coating formulation and strategy was optimized. A drug formulation of 16 wt% PAT and 4% wt/vol PEO, a polymer formulation of 2.5% wt/vol PEO, and a total of two drug layers produced a mostly uniform and thin coating with no defects and acceptable drug load. The balloon also had optimal drug uptake in arterial tissue in an in vitro flow model. Next, the reproducibility of the coating strategy was improved by optimizing the instrument parameters. The optimized instrument parameters (translational speed = 0.150 in/s, revolution rate = 100 rpm, flow rate = 0.6 ml/min) resulted in improved reproducibility of the drug load and similar coating properties as the DCB. This study demonstrated the ability to automate the micropipette process to obtain a balloon with optimal coating properties and drug tissue uptake.