Brussels Airport Warns of Border Control Delays as EU Entry/exit System Goes Live

(BRUSSELS, BELGIUM) — Brussels Airport warned that the new EU Entry/Exit System is causing long border control delays for non-EU passengers, with waits of up to 1 hour on departure and nearly 2 hours on arrival as of late March 2026.

The airport said the disruption stems from longer processing times for each traveler and the suspension of e-gates for nationals from the United States, United Kingdom, Canada, and Singapore. That change has forced all non-EU travelers through manned counters.

Pressure has persisted even after changes to how the system is being introduced. On the morning of April 1, 2026, waits were still 1 hour at departure and nearly 2 hours at arrival.

Those delays follow a sharper bout of disruption in late March 2026, when non-European passengers faced up to 2 hours at departures and over 3 hours at arrivals, with a peak of 3.5 hours. Over four days, the disruption led to nearly 600 missed flights and 21 total hours of delays.

The bottlenecks center on the EU Entry/Exit System, a digital border management system for non-EU nationals crossing the Schengen area’s external borders. It records personal and biometric data, including fingerprints and facial images for those over 12, along with entry and exit dates and places.

The system is replacing manual passport stamps and tracking short stays across participating countries. Its phased rollout began October 12, 2025, and full application is due by April 10, 2026.

At Brussels Airport, the system applies to both arrivals and departures. The airport has 61 pre-registration kiosks and additional booths in place for processing.

Travelers who refuse to provide biometrics can be denied entry. At the same time, Brussels Airport has 36 e-gates on order for EES biometric enrollment, though the current suspension has removed e-gate access for several large groups of third-country nationals.

That has widened the strain on staffed counters at a busy external border point. Nationals from the United States, United Kingdom, Canada, and Singapore, who would otherwise use automated lanes, now require manual processing.

The scale of the backlog became especially clear in the final days of March. As of March 30, 2026, 100% of passengers had to register in EES without biometrics, after previous operations ran at 60% capacity.

Even that adjustment did not clear the queues. Brussels Airport said lines persisted after Ministers Quintin and Van Bossuyt postponed biometric data registration.

A separate failure earlier in the year showed how quickly delays can spread across the airport’s border control system. On February 6-7, 2026, a software glitch disabled all 24 e-gates in non-Schengen arrivals.

That outage caused 90-minute queues at peak times and forced officers to carry out manual passport checks. EU, EEA and Swiss citizens are not covered by EES, but they also faced indirect delays during the February glitch.

For Brussels Airport, the current problem is not a single breakdown but the slower pace of the new process itself. Each extra minute at inspection points reduces the number of passengers that officers and border posts can handle.

The airport has urged Belgian ministers to press the European Commission for a more flexible EES rollout, especially before summer traffic peaks. It has also called for full federal police staffing at all border posts and for e-gates to resume for third-country nationals.

Those requests point to two pressures running at once: the demands of the new digital system and the basic need for enough staff and automated capacity to keep queues moving. With full application of EES set for April 10, 2026, the timing leaves little room for the airport to absorb more disruption before heavier seasonal traffic.

Brussels Airport has advised travelers on non-Schengen flights to arrive 3 hours early. It also told passengers to monitor airline alerts.

That advice reflects the way delays now affect both ends of a journey. Departing travelers face longer waits before reaching their gates, while arriving passengers can spend extended periods in passport control before entering Belgium.

Non-EU passengers are likely to feel the greatest impact because EES applies directly to them. The system records fingerprints and facial images, along with entry and exit details, and those steps take longer than traditional stamp-based checks.

Manual processing becomes even slower when automated channels are unavailable. The suspension of e-gates for some of Brussels Airport’s most common non-EU nationalities has therefore increased the volume at counters that were already handling the new registration process.

The figures from late March show how quickly the impact can build. Queues of over 3 hours at arrivals, with a peak of 3.5 hours, did not stay confined to passport control but spilled into missed connections and missed departures, producing nearly 600 missed flights in four days.

Those missed flights came alongside 21 total hours of delays. Even after the late-March peak eased, the April 1 waiting times showed that border control delays had not disappeared.

The rollout schedule helps explain why the airport is seeking flexibility. EES began in phased form on October 12, 2025, and moves to full application by April 10, 2026 across participating countries.

That leaves airports and border agencies little time to smooth out technical and staffing issues before the system reaches full scope. Brussels Airport has pointed to similar queues in other EU countries as it argues that operations need to run smoothly first.

The airport’s request to resume e-gates for third-country nationals is also tied to that transition. Automated lanes can process passengers faster, but the current suspension means many travelers who might have been screened electronically now join manual lines.

The 36 e-gates on order for EES biometric enrollment show that Brussels Airport is building for the new system. For now, though, the airport is operating with a gap between the border process EES requires and the automated capacity needed to handle it at speed.

That gap widened again when all 24 e-gates in non-Schengen arrivals failed during the February 6-7, 2026 software glitch. The incident showed that even travelers outside the system’s direct scope can be caught in wider congestion once border posts switch to manual checks.

For passengers, the practical effect is straightforward. Non-EU travelers should prepare for continued border control delays at Brussels Airport until the system becomes more stable.

They may also need to plan for manual processing even when they would normally expect to use e-gates. For EU, EEA and Swiss citizens, EES does not apply, but they can still encounter slower movement through the airport when glitches or staffing pressures affect the broader border control area.

Brussels Airport’s current guidance remains unchanged: arrive 3 hours early for non-Schengen flights and keep track of airline communications. With the EU Entry/Exit System nearing full implementation, border control delays remain part of the journey for many passengers passing through Brussels Airport.