SAN Airport Security: Checkpoints, PreCheck and CLEAR

SAN's advice is to arrive at least 2 hours before a domestic flight and 3 hours before an international flight.

The airport is open around the clock, but SAN says departures only occur without penalty between 6:30 a.m. and 11:30 p.m., so there are no overnight flights. The gate areas close around 2 a.m. each night, and everyone has to wait on the pre-security side. Ticket counters and security checkpoints reopen at about 4:15 a.m. Airlines with morning flights usually staff their ticket counters by 4:30 a.m., and each airline sets its own hours. SAN's airline directory lists Southwest ticket counters open 4:15 a.m. to midnight and Alaska 4 a.m. to midnight.

So if your flight is at 6:30 a.m., you will not clear security before about 4:15 a.m. no matter how early you show up.

• Terminal 1: one main checkpoint, after ticketing.
• Terminal 2 East: its own checkpoint, for airlines on the East side.
• Terminal 2 West: its own checkpoint, for airlines on the West side. SAN says CLEAR is available at Checkpoint 6 (Terminal 2 West).

SAN says Terminal 2 checkpoints are split by airline location. Your boarding pass or airline app shows your terminal, and your airline's ticket counter tells you which side you are on.

SAN does not publish separate opening hours for each checkpoint. The only published time is that checkpoints reopen at about 4:15 a.m. after the overnight closure. If you have an early or late flight, check with your airline for the exact times.

TSA PreCheck is available in both Terminal 1 and Terminal 2. Eligible travelers can keep shoes, belts and light jackets on, and leave laptops and liquids in their bags. Add your Known Traveler Number to your airline reservation so the PreCheck mark prints on your boarding pass.

CLEAR+ uses biometric screening in place of the ID check, then you go to physical screening. It requires a membership and works alongside PreCheck. SAN's security page lists CLEAR+ at Terminal 2 East from 4 a.m. to 7:30 p.m. daily.

CLEAR announced a lane in the new Terminal 1 on September 23, 2025. SAN's own pages disagree on the rest: its services page puts CLEAR at the Terminal 1 and Terminal 2 West checkpoints, its security page lists Terminal 2 East, and its terminals page names Checkpoint 6 in Terminal 2 West. Check clearme.com or the CLEAR app for your terminal and hours before you plan around it.

We did not find a live security wait time on SAN's website, and SAN does not list a program for reserving a security time slot. SAN does warn that heightened TSA measures can lead to longer waits at the checkpoints.

For a wait estimate, use the MyTSA app or your airline's app, and plan around SAN's 2 hour rule for domestic flights.

SAN's security page lists these reminders:

• You need a REAL ID compliant driver's license or another accepted federal ID to board a U.S. commercial flight. REAL ID has been required since May 7, 2025.
• Other accepted IDs include U.S. passports, military IDs and DHS trusted traveler cards such as Global Entry or NEXUS.
• SAN says TSA began offering a fee based TSA Confirm ID service on February 1, 2026 for travelers who cannot show approved ID.
• Liquids: 3.4 oz (100 mL) per item, all in one quart sized bag.
• Laptops come out of your bag unless you use PreCheck.
• Lithium batteries go in your carry-on, not your checked bag.
• Medications and baby items are exempt from the liquid limit but can be inspected.

Not sure about an item? SAN points to the TSA searchable database of what you can bring.

If you are not flying, you can still go through security with a SAN Pass. Apply online at gatepass.san.org/san, the same day or up to 7 days ahead. TSA reviews each request, and the pass arrives by email as a PDF to show with a photo ID.

SAN Pass holders enter through general screening at the TSA checkpoints in Terminal 1 or Terminal 2 between 4 a.m. and 9 p.m. The pass cannot be combined with TSA PreCheck or CLEAR. Passes are limited each day and the program can change.

• TSA Cares: a helpline for travelers with disabilities, medical conditions or special needs. Contact TSA at least 72 hours before your flight. The number is 855.787.2227.
• General TSA questions: 866.289.9673, or text Ask TSA at 275.872.
• Wheelchair help is arranged through your airline, ideally before you travel.
• SAN Assist is for travelers with non-visible disabilities. A Travel Guide can be requested at least 3 business days ahead and is available daily from 6 a.m. to 10 p.m. A familiarization tour should be requested 2 to 3 weeks ahead and runs Monday to Friday during business hours. All services depend on availability.

Terminal 1 is being rebuilt. SAN says the original Terminal 1 is permanently closed and being demolished, and Phase 1B of the new terminal is scheduled to be complete in 2028. SAN's project page lists a 13 lane security checkpoint for the finished new Terminal 1. Today SAN describes Terminal 1 as having one main checkpoint. Check san.org before you travel for any change.

SAN says the roadway between Terminals 1 and 2 will be closed to all traffic. If you are in the wrong terminal, take the free Inter-Terminal Shuttle, which runs daily from 4 a.m. to 2 a.m.