This paper discusses the laser-irradiated microjoints between glass and polyimide for applications in neural implants. To facilitate bonding between them, a thin titanium film with a thickness of approximately 0.2 μm was deposited on glass wafers using the physical vapor deposition (PVD) process. Two sets of samples were fabricated where the bonds were created using diode and fiber lasers. The samples were subjected to tension using a microtester for bond strength measurements. The failure strengths of the bonds generated using fiber laser are quite consistent, while a wide variation of failure strengths are observed for the bonds generated with diode laser. Few untested samples were sectioned and the microstructures near the bond areas were studied using an optical microscope. The images revealed the presence of a sharp crack in the glass substrate near the bond generated with the diode laser. However, no such crack was observed in the samples made using fiber laser. To investigate the reasons behind such discrepancy in bond quality further, uncoupled three-dimensional finite element analyses (FEA) were conducted only for the samples created using diode laser. First, the transient heat diffusion-based FEA was conducted by using the laser power intensity distribution as a time dependent heat source. This model calculates the temperature distribution within the substrates as a function of time. Next, the structural model predicts the amount of residual stresses developed in the joint system as it is cooled down to room temperature. The out-of-plane normal component of residual stresses was within the failure strength range of glass that may have caused fracture initiation in the substrate.