Zirconium-89 (89Zr) can be produced in a cyclotron by focusing the proton beam on an yttrium-89 (89Y) foil target. Optimal combination of beam energy and target assembly configuration enables maximum production of 89Zr while minimizing the formation of contaminant nuclides such as 88Zr and 88Y to allow efficient and effective radiopharmaceutical labeling. Accurate modeling of the proton beam and the target is therefore an essential step to assure the best beam and target specification. We used the radiation transport code MCNPX to simulate the transport of protons through the irradiation assembly and the nuclear reaction code TALYS to obtain the production cross sections of various nuclides from proton-89Y reactions. Results from simulating the irradiation of 14 mm diameter targets with aluminum (Al) degrader at 19.8 mA for 1 h suggested that the 0.15 mm thick one would produce 227 MBq while the 0.3 mm thick one would produce 413 MBq of 89Zr with less than 1 % uncertainty. These results show excellent agreement with experimental work in literature. This work provides the basis for further experimental and theoretical assessments of the use of 89Zr as radiopharmaceutical labels.