The Islamists are Jordan's main opposition group and have considerable grassroots support, but their relations with the authorities have been strained over the demands for political reforms.
The IAF boycotted the previous elections in protest at the electoral system which they say weakens political parties in favour of tribal and other pro-government candidates.
Party chief Mohamed Zyoud told a news conference that the Islamists believe it is "their national duty" to take part in legislative polls slated for September 20, even in the absence of reforms.
Zyoud called for "transparency" during the election and "for an end to intervention by the authorities throughout the voting process and the announcement of the results".
Jordan amended its electoral law in March to allow political parties to submit lists, and divided the tiny desert kingdom into 23 electoral districts.
The number of seats in parliament was also reduced from 150 to 130, with 15 reserved for women.
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Jordanian authorities view the Brotherhood as an illegal organisation because its licence was not renewed in accordance with a political parties law adopted in 2014.
But the IAF is not bound by any restrictions.
Relations with the government soured after the 2011 Arab Spring uprisings that shook the region, toppling leaders in several countries.
Last year the Brotherhood's second-in-command Zaki Bani Rsheid was sentenced to 18 months in prison for criticising a decision by the United Arab Emirates to blacklist the group. He was freed in January.
Also last year, the government authorised the formation of a breakaway group known as the Muslim Brotherhood Association, sparking accusations that it was seeking to weaken the organisation.
In April this year authorities shut seven Brotherhood offices across Jordan.
The Islamists won only six seats in the 2007 election.