The Brotherhood's stated goal is to instill the Qur'an and Sunnah as the "sole reference point for ... ordering the life of the Muslim family, individual, community ... and state". Since its inception in 1928 the movement has officially opposed violent means to achieve its goals, with some exceptions such as in the Israeli-Palestinian conflict or to overthrow secular Ba'athist rule in Syria (see Hama massacre). This position has been questioned, particularly by the Egyptian government, which accused the group of a campaign of killings in Egypt after World War II.

The Muslim Brotherhood is banned in Egypt, and members have been arrested for their participation in it. As a means of circumventing the ban, supporters run for office as independents. The Egyptian government in one case responded by obstructing voters, despite Egyptian President Hosni Mubarak's promise to have a "free and fair election."

Outside of Egypt, the group's political activity has been described as evolving away from modernism and reformism towards a more traditional, "rightist conservative" stance.  For example, the Muslim Brotherhood party in Kuwait opposes suffrage for women. The Brotherhood condemned terrorism and the 9/11 attacks, but whether or not it has ties to terrorism is a matter of dispute. Its position on violence has also caused disputes within the movement, with advocates of violence at times breaking away to form groups such as the Al-Gama'a al-Islamiyya (The Islamic Group) and Al Takfir Wal Hijra (Excommunication and Migration).

Among the Brotherhood's more influential members was Sayyid Qutb. Qutb was the author of one of Islamism's most important books, Milestones, which called for the restoration of Islam by re-establishing the Sharia and by using "physical power and Jihad for abolishing the organizations and authorities of the Jahili system," which he believed to include the entire Muslim world. While studying at university, Osama bin Laden claimed to have been influenced by the religious and political ideas of several professors with strong ties to the Muslim Brotherhood including both Sayyid Qutb and his brother Muhammad Qutb. However, once Al Qaeda was fully organized, they denounced the Muslim Brotherhood's reform through nonviolence and accused them of "betraying the cause of Islam and abandoning their 'jihad' in favour of forming political parties and supporting modern state institutions".

The Brotherhood is financed by contributions from its members, who are required to allocate a portion of their income to the movement. Some of these contributions are from members who live in oil-rich countries.

In the group's belief, the Quran and Sunna constitute a perfect way of life and social and political organization that God has set out for man. Islamic governments must be based on this system and eventually unified in a Caliphate. The MB goal, as stated by Brotherhood founder Hassan al-Banna was to reclaim Islam’s manifest destiny, an empire, stretching from Spain to Indonesia. It preaches that Islam enjoins man to strive for social justice, the eradication of poverty and corruption, and political freedom to the extent allowed by the laws of Islam. The Brotherhood strongly opposes Western colonialism, and helped overthrow the pro-western monarchies in Egypt and other Muslim nations during the early 20th century.

On the issue of women and gender the Muslim Brotherhood interprets Islam very traditionally. Its founder called for "a campaign against ostentation in dress and loose behavior," "segregation of male and female students," a separate curriculum for girls, and "the prohibition of dancing and other such pastimes..." The MB is a movement, not a political party, but members have created political parties in several countries, such as the Islamic Action Front in Jordan and Hamas in Gaza and the West Bank. These parties are staffed by Brotherhood members but kept independent from the MB to some degree.

From transcripts the following hierarchical Organisation structure can be derived:

It has the following divisions (not complete): – Executive leadership – Organisational office – Secretariat general – Education office – Political office – Sisters office

In each country there is a Branch committee with a Masul (leader) appointed by the General Executive leadership with essentially the same Branch-divisions as the Executive office has. To the duties of every branch belong fundraising, infiltrating in and overtaking other Muslim organisations for the sake of uniting the Muslims to dedicate them to the general goals of the MB.