As an intermediate half-life positron emitter (86)Y is an attractive radioisotope for positron emission tomography (PET) studies, particularly for patient specific dosimetry planning of (90)Y-based radiotherapy procedures. It can be conveniently produced by a small-sized cyclotron via the (86)Sr(p,n)(86)Y nuclear reaction. The optimization of the electrochemical separation of (86)Y from the target material and its purification was done by modeling the whole production cycle using (90)Y. The radionuclide was isolated using four electrodes in two electrolytic steps. In the first step two Pt plate anodes and a Pt Winkler cathode were used and the electro-deposition yield was determined in constant current mode of operation. In addition, the influence of pH on the efficiency of this first step was investigated. The second electrolysis, with Winkler electrode as anode and a Pt wire as cathode, was also performed in constant current mode of operation. The kinetics of recovery of the deposited activity on the Pt wire was investigated in acidic solutions. The optimized electrochemical method was then applied for (86)Y separation and purification. This modified procedure was proved to be faster and simpler than the previously proposed electrochemical techniques and is more convenient for automation of the routine production of (86)Y.