Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia and significantly increases the risk of stroke. Left atrial catheter ablation (LACA), utilising techniques like cryoablation and radiofrequency ablation, is commonly employed to restore sinus rhythm, which helps normalise atrial function and reduce blood stasis, thereby lowering the risk of thrombus formation and stroke. While these procedures are effective in restoring normal rhythm, cases of thrombus formation during ablation have been reported. Certain regions of the atrium appear more susceptible to thrombus development. To investigate this, computational fluid dynamics (CFD) and thrombogenesis models were used to simulate blood flow patterns, temperature distributions, non-Newtonian blood behaviour, and coagulation processes in both cryoablation and radiofrequency ablation scenarios. This study found no significant difference in flow characteristics or thrombogenicity between cryoablation and radiofrequency ablation. However, the right inferior pulmonary vein (RIPV) and the posterior wall of the left atrium (LA) were identified as two regions, commonly targeted during LACA, that are particularly prone to thrombus formation. Furthermore, the incorporation of non-Newtonian blood behaviour in the flow model revealed a correlation between exacerbated flow metrics and increased thrombogenicity, emphasising the relationship between non-Newtonian blood properties and stroke risk. This novel approach offers a promising framework for future studies, which could refine these models to better understand the mechanistic factors contributing to periprocedural stroke risk during LACA.