Corneal cross-linking (CXL) is a well-established treatment for corneal ectasias, primarily keratoconus, enhancing stromal rigidity and halting disease progression. While generally safe, CXL is associated with complications that require prompt recognition and management. Early-onset issues, such as pain, delayed epithelial healing, and keratitis, are primarily linked to epithelial debridement in traditional epi-off protocols. Late-onset complications include transient stromal haze, hyperopic shifts, and continued ectasia progression, often influenced by preoperative corneal parameters. Advances in epi-on techniques have mitigated some risks, offering improved patient comfort and reduced complications, albeit with historically lower efficacy. This review explores common and rare complications of CXL, emphasizing their pathophysiology, risk factors, and management strategies. Understanding these challenges is essential for optimizing outcomes, particularly in high-risk cases, such as advanced keratoconus or thin corneas. Future innovations, including customized protocols, aim to refine the balance between safety and efficacy.