Background: Selecting enterprise resource planning (ERP) systems for complex port environments is a significant challenge. This study addresses a key research gap by identifying and prioritizing the critical factors for ERP selection within the strategic context of United Arab Emirates (UAE) ports, which function as vital hubs in global trade. Methods: A hybrid methodology was employed, first using the Fuzzy Delphi Method (FDM) to validate thirteen challenges with five industry experts. Subsequently, the Relative Importance Index (RII) was used to rank these challenges based on survey data from 48 UAE port professionals. Results: The analysis revealed “Cybersecurity concerns” as the highest-ranked challenge (RII = 0.896), followed by “Engagement with external stakeholders” (RII = 0.842), and both “Process optimization” and “Technical capabilities” (RII = 0.808). Notably, factors traditionally seen as critical in other sectors, such as “Organizational readiness” (RII = 0.746), were ranked significantly lower. Conclusions: The findings indicate a strategic shift in ERP selection priorities toward digital resilience and external integration rather than internal organizational factors. This research provides a sector-specific decision-support framework and offers actionable insights for port authorities, vendors, and policymakers to enhance ERP implementation in the maritime industry.