The attacks on the Pentagon and World Trade Center on September 11, 2001 caused an immediate deployment of US special operations forces, and the SEALs were no exception. At least seven separate platoons from SEAL Teams Two, Three, and Eight served in Afghanistan as well as parts of SEAL Delivery Vehicle Team One.

Operating by themselves or jointly with other US or allied forces as part of the Coalition Joint Special Operations Task Force, SEALs were deployed to the mideast, operating in Pakistan and Afghanistan. Members of SEAL Delivery Vehicle Team One performed reconnaissance for a possible amphibious landing in Pakistan, gaining hydrographic intel as well as information on a nearby airport. VBSS missions were carried out by SEALs attached to the USS Shreveport LPD-12 to ensure no weapons were being smuggled into Afghanistan by sea. Members of SEAL Team 3 were inserted into Afghanistan by US Special operations aircraft and observed the small airfield that would later become Camp Rhino for four days prior to the Marines landing there. Just prior to the Marines' arrival the SEALs marked the airfield and provided security while the aircraft approached.

SEALs also operated with members of the US Army's 1st SFO(D) as part of "Task Force 11" hunting down members of the Taliban government and Al Qaeda leadership. SEALs performed reconnaissance missions, lying in observation posts or actively scouting in what were known as SSE (Sensitive Site Exploitation) missions. Platoons from SEAL Teams Two, Three, and Eight operated in Afghanistan, sometimes using Desert Patrol Vehicles carried in by helicopters but also patrolling on foot after helicopter insertion.

In January of 2002 a planned simple 12 hour intelligence gathering mission turned into a nine-day bonanza of exploration and destruction. Nearly a million pounds of ammunition and equipment was found in an extensive network of seventy caves and tunnels in a narrow valley at Zhawar Kili in eastern Afghanistan, near the Pakistan border. Some of the tunnels were brick-lined and supported by steel I-beams and the entire complex, above ground and below, was so large and complex that Chenowth Fast Attack Vehicle were flown in to help provide support. The amount of intelligence was overwhelmingly more than expected, and the SEALs were reinforced by US Marines to provide protection while they focused on exploring and destroying the complex.

Some of the explosives and equipment were blown in place but the heavier vehicles had to be destroyed by precision guided munitions dropped by Navy aircraft. In all, more than 400,000 pounds ordinance was dropped on targets designated by SEALs and EOD members. In the end, the SEALs had helped deny Al Qaeda not only weapons and munitions, but also communications networks, training classrooms, living quarters, and office space filled with paperwork. This operation also proved again the high level of ability of the SEALs; due to the planned short nature of the operation the SEALs had gone in light and had to operate for over two days before they could be resupplied with water, food, and supplies.

SEALs partnered with Danish Special Forces in the capture of Taliban Mullah Khairullah Kahirkhawa in February of 2002. Operators of a Predator reconnaissance vehicle orbiting the hills in the Paktia province had seen the Mullah leave a building and radioed the headquarters at Camp Rhino. SEALs and Danish commandos quickly loaded a US Air Force MH-53M Pave Low and headed out within fifteen minutes with an Army AH-64A Apache as escort. An hour and a half after the first notice, the Mullah was on the ground in US custody.

Early March saw a batttle that caused the greatest number of US special operations forces casualties during Enduring Freedom, including SEALs. The battle at Takur Ghar began when two Army MH-47E's attempted to drop SEAL teams at observation posts on hills overlooking the Shah-e-Kot valley. One aircraft, call sign Razor 03, approached a landing zone on top of the Takur Ghar mountaintop at 0300 on March 2, 2002. Observing fresh signs of occupation, the crew and operators quickly began talking about aborting the insertion, but were quickly taken under fire but well concealed and dug-in enemy forces. An RPG round slammed into the side of the aircraft, followed by heavy machine fire which ruptured hydralic and oil lines. With lurching, rough motions the pilots managed to get the aircraft under control and headed away from the LZ but in doing so one SEAL and a helicopter crewmember were thrown off balance and slipped off of the aircraft's slick rear ramp. The crew member was attached to the aircraft and was hauled back aboard, but ABH1 Neal Roberts was not and fell five to ten feet to the snow below.

This started off a chain of events that ultimately saw five US dead and eleven wounded. Razor 03 had to be crash landed at close to where they had taken fire and a quick headcount revealed what the crew member had told them; he was not the only passenger than had fallen. The survivors of Razor 03 were picked up by Razor 04, another MH-47 and returned to the mountain top. Roberts' teammates were unable to locate him and then were taken under fire themselves. The Air Force Combat Controller was hit and mortally wounded by gunfire and two of the SEALs were wounded by enemy fire and grenades. With half of their force casualties the SEALs decided to break contact and retire. An Army Ranger Quick Reaction Force which landed soon after had one of their two helicopters shot down on the mountain top as well and took heavy casualties while clearing the mountaintop of enemy forces and preventing their reinforecement.

Casualties, while not as heavy as some of the losses in earlier actions, proved that Navy SEALs operate on the edge in a very dangerous environment. In addition to Roberts and the two SEALs wounded at Takur Ghar, another SEAL, CPO Matthew Bourgeois was killed and another SEAL wounded by an enemy mine on March 28, 2002 during breaching training at Tarnak Farms near Kandahar. Two SEALs were wounded September 1, 2002 in an intelligence gathering mission in the Oruzgan province of Southern Afghanistan.

SEAL involvement in Afghanistan is not yet complete and it will take many years before the full extent of their actions is fully known by the general public.