Purpose: To investigate the efficacy of non-penetrating femtosecond laser intrastromal astigmatic keratotomy (ISAK) in terms of topographic and refractive changes. Methods: Retrospective study including 42 eyes (35 patients) with a corneal astigmatism between 0.5 and 1.5 D. All eyes underwent femtosecond laser-assisted cataract surgery with ISAK for astigmatism management using the Catalys laser system (Johnson & Johnson Vision). Visual acuity, refraction, as well as corneal topographic and corneal endothelial cell density (ECD) changes were evaluated during a 12-month follow-up. Astigmatic changes were analyzed using the Alpins vector method. Results: A significant reduction in manifest cylinder was observed at 1 month postoperatively (p = 0.03), with no significant changes afterwards (p = 0.90). A total of 38.1%, 52.4% and 59.2% of eyes had a manifest cylinder of 0.50 D or lower preoperatively and at 1 and 12 months after surgery, respectively. A significant reduction was found in topographic astigmatism at 1 month postoperatively (p < 0.01), with an additionally small but statistically significant reduction afterwards (p < 0.01). No significant changes in postoperative uncorrected (p = 0.97) and corrected visual acuities (p = 0.40) were observed during the follow-up. There was a trend to undercorrection of corneal astigmatism that decreased significantly over time. This led to some variability in changes of refractive astigmatism. A small but significant reduction in ECD was observed at 1 month postoperatively (p < 0.01), with no significant changes afterwards. Conclusions: Femtosecond laser assisted ISAK is an effective and safe option to reduce corneal astigmatism during cataract surgery and consequently refractive astigmatism.