Israel had completed its final offensive in the Golan Heights, and a ceasefire was signed the day after. Israel had seized the Gaza Strip, the Sinai Peninsula, the West Bank of the Jordan River (including East Jerusalem), and the Golan Heights. Overall, Israel's territory grew by a factor of three, including about one million Arabs placed under Israel's direct control in the newly captured territories. Israel's strategic depth grew to at least 300 kilometers in the south, 60 kilometers in the east and 20 kilometers of extremely rugged terrain in the north, a security asset that would prove useful in the Yom Kippur War six years later.

The political importance of the 1967 Six Day War was immense; Israel demonstrated that it was not only able, but also willing, to initiate strategic strikes that could change the regional balance. Egypt and Syria learned tactical lessons and would launch an attack in 1973 in an attempt to reclaim their lost territory.

Speaking three weeks after the war ended, as he accepted an honorary degree from Hebrew University, Yitzhak Rabin gave his reasoning behind the success of Israel:

Our airmen, who struck the enemies' planes so accurately that no one in the world understands how it was done and people seek technological explanations or secret weapons; our armored troops who beat the enemy even when their equipment was inferior to his; our soldiers in all other branches...who overcame our enemies everywhere, despite the latter's superior numbers and fortifications-all these revealed not only coolness and courage in the battle understanding that only their personal stand against the greatest dangers would achieve victory for their country and for their families, and that if victory was not theirs the alternative was annihilation.

In recognition of contributions, Rabin was given the honor of naming the war for the Israelis. From the suggestions proposed, he "chose the least ostentatious, the Six-Day War, evoking the days of creation."

Dayan's final report on the war to the Israeli general staff listed several shortcomings in Israel's actions, including misinterpretation of Nasser's intentions, overdependence on the United States, and reluctance to act when Egypt closed the Straits. He also credited several factors for Israel's success: Egypt did not appreciate the advantage of striking first and their adversaries did not accurately gauge Israel's strength and its willingness to use it.

After the 1973 Arab-Israeli War, Egypt reviewed the causes of its loss of the 1967 war. Issues that were identified included "the individualistic bureaucratic leadership"; "promotions on the basis of loyalty, not expertise, and the army's fear of telling Nasser the truth"; lack of intelligence; and better Israeli weapons, command, organization, and will to fight.

According to Chaim Herzog:

On June 19, 1967, the National Unity Government [of Israel] voted unanimously to return the Sinai to Egypt and the Golan Heights to Syria in return for peace agreements. The Golans would have to be demilitarized and special arrangement would be negotiated for the Straits of Tiran. The government also resolved to open negotiations with King Hussein of Jordan regarding the Eastern border.

The Israeli decision was to be conveyed to the Arab nations by the United States. The US was informed of the decision, but not that it was to transmit it. There is no evidence of receipt from Egypt or Syria, and some historians claim that they may have never received the offer.

In September, the Khartoum Arab Summit resolved that there would be "no peace, no recognition and no negotiation with Israel." However, as Avraham Sela notes, the Khartoum conference effectively marked a shift in the perception of the conflict by the Arab states away from one centered on the question of Israel's legitimacy toward one focusing on territories and boundaries and this was underpinned on November 22 when Egypt and Jordan accepted United Nations Security Council Resolution 242.

The June 19 Israeli cabinet decision did not include the Gaza Strip, and left open the possibility of Israel permanently acquiring parts of the West Bank. On June 25–27, Israel incorporated East Jerusalem together with areas of the West Bank to the north and south into Jerusalem's new municipal boundaries.

Yet another aspect of the war touches on the population of the captured territories: of about one million Palestinians in the West Bank, 300,000 (according to the United States Department of State) fled to Jordan, where they contributed to the growing unrest. The other 600,000 remained. In the Golan Heights, an estimated 80,000 Syrians fled.[175] Only the inhabitants of East Jerusalem and the Golan Heights became entitled to receive full Israeli citizenship, as Israel applied its law, administration and jurisdiction to these territories in 1967 and 1981 respectively, and the vast majority in both territories declined to do so. See also Israeli-Palestinian conflict and Golan Heights. Both Jordan and Egypt eventually withdrew their claims to the West Bank and Gaza (the Sinai was returned on the basis of Camp David Accords of 1978 and the question of the Golan Heights is still being negotiated with Syria). After Israeli conquest of these newly acquired 'territories,' a large settlement effort was launched to secure Israel's permanent foothold. There are now hundreds of thousands of Israeli settlers in these territories, though the Israeli settlements in Gaza were evacuated and destroyed in August 2005 as a part of Israel's unilateral disengagement plan.

The 1967 War also laid the foundation for future discord in the region - as on November 22, 1967, the UN Security Council adopted Resolution 242, the "land for peace" formula, which called for Israeli withdrawal "from territories occupied" in 1967 and "the termination of all claims or states of belligerency."

Resolution 242 recognized the right of "every state in the area to live in peace within secure and recognized boundaries free from threats or acts of force." Israel returned the Sinai to Egypt in 1978, after the Camp David Accords, and disengaged from the Gaza Strip in the summer of 2005, though its army frequently re-enters Gaza for military operations and still retains control of border crossings, seaports and airports.

The aftermath of the war is also of religious significance. Under Jordanian rule, Jews were effectively barred from visiting the Western Wall (even though Article VIII of the 1949 Armistice Agreement demanded Israeli Jewish access to the Western Wall). Jewish holy sites were not maintained, and their cemeteries had been desecrated. After the annexation to Israel, each religious group was granted administration over its holy sites. Despite the Temple Mount's importance in Jewish tradition, the al-Aqsa Mosque is under sole administration of a Muslim Waqf, and Jews are barred from conducting services there.