The tunnel is designed with a single highway lane. The floor of the tunnel is constructed of 1,800 texturized concrete panels (each 7.5 feet (2.3 m) by 8 feet (2.4 m)) with the railroad tracks sunken slightly below the road surface. The interior is exposed rock, and contains several "safe-houses", which are small buildings that are used in case of severe earthquakes, vehicle fires, or other emergencies. The tunnel also contains several pull-outs, which are reserved for disabled vehicles. As motor vehicle speed in the tunnel is limited to 25 miles per hour (40 km/h), it takes about ten minutes to travel from end to end.

The tunnel uses a combination of portal fans and reversible jet fans to ensure proper air flow and air quality throughout the tunnel. There are two backup generators to ensure that the computerized traffic controls and safe-house ventilation systems in the tunnel continue to function in the event of a power failure. Because eastbound traffic, westbound traffic, and the Alaska Railroad must share the tunnel, rail and road traffic are coordinated by two computer-based systems — the Tunnel Control System and the Train Signal System.

These systems control the timing of vehicles entering the tunnel, spacing them for safety, and lower railroad gates when a train is approaching. The tunnel's entrance portals are designed in an A-shape, with a large, train-sized "garage door", which allows traffic in and out of the tunnel. The entrance portals are designed to withstand the force of an avalanche. The tunnel's eastern terminus is in Whittier. The staging areas on either side of the tunnel can accommodate as many as 450 vehicles waiting to pass through.

According to  wikipedia