This study presents the optimized design of the axial injection beamline for the SKKUCY-350 superconducting cyclotron, currently under development at Sungkyunkwan University, South Korea. The cyclotron is designed to accelerate ions such as \({}^{12}{\text{C}}^{6+}, {\text{H}}_{2}^{+}\) , and \({}^{4}{\text{He}}^{2+}\) to energies of up to 350 MeV/nucleon for applications in hadron therapy. The injection beamline faces significant challenges due to the cyclotron’s strong stray and fringe magnetic fields, which can lead to substantial beam losses. To address these challenges, a comprehensive magnetic shielding system, referred to as the Gauss chamber, was designed to attenuate the stray magnetic field. Initial beamline optimization was performed using a 2D code, and a full 3D model was subsequently created using TOSCA 3D to validate and refine the design. The integration of 3D simulations was critical in accurately modeling the complex magnetic field environment and validating the effectiveness of these design modifications. A key innovation of this work is a modified axial hole geometry. This non-uniform profile actively suppresses beam envelope oscillations, significantly enhancing the stability of the injected beam.