El-Sisi made his remarks during a meeting with a number of media professionals on the sidelines of the inauguration of the country's light rail transit (LRT).
The national dialogue, which El-Sisi called during the annual Egyptian Family Iftar banquet on 26 April for “all political forces without any exceptions or discrimination," is set to begin on Tuesday with a meeting of its board of trustees.
A myriad of political parties and forces have welcomed the step and expressed willingness to join the dialogue.
The General Coordinator of the National Dialogue Diaa Rashwan has affirmed that no one will be excluded from the national dialogue except those who have blood on their hands or carried out terrorism or violence.
The administration of the national dialogue announced in late June a diverse board of trustees that include parliamentarians, journalists, professors and officials.
The Muslim Brotherhood were ousted from power on 3 July 2013 after sweeping nationwide demonstrations against its rule from 30 June to 3 July.
The group, which unleashed a widespread campaign of terror against police and army personnel as well as deadly attacks on churches after its ouster from power, was designated a terrorist group in December 2013.
During the meeting on Monday, El-Sisi explained that the Muslim Brotherhood are excluded from the national dialogue because they turned down the proposal in July 2013 to hold early presidential elections to resolve the crisis at the time and opted to attempt to rule by force.
"On 3 July we presented them with a vision to overcome their crisis... by holding early presidential elections.
"The people went out on the streets... we said let's give them a chance to express their opinion... but they (the Muslim Brotherhood) insisted they have supporters and that this was a conspiracy.
"We said let's see if it really is a conspiracy and hold early presidential elections."
The president added, "we said if people vote for you again then okay ... and if they don't, you can remain part of the political process in Egypt. This did not happen... they chose war."
If one [chooses] warring then there is no common ground for dialogue and discussion, the president stressed.
"We were talking about dialogue and they were talking about killing," El-Sisi stated.
The idea of holding a national dialogue to find a way out was not on the Muslim Brotherhood's agenda at the time and they wanted to run the country by force, he added.
El-Sisi stressed on Sunday in a message to the nation on the ninth anniversary of 30 June Revolution that the 3 July 2013 decision was a turning point in the history of Egypt, the region, and the world.
Egypt was heading down a road of no return at the time, El-Sisi added, pointing out that some countries that took the same road suffered from chaos.
The president said they [Muslim Brotherhood group] did not understand the meaning of a state and all what they thought about was how to incite people on the street.
President El-Sisi accused the Muslim Brotherhood group of destroying the state's potential over the period of 18 months of their rule.
He described the protest of 35 million Egyptians against the Muslim Brotherhood on 30 June 2013 as a "blessing" from God.
President El-Sisi said the situation after the 3 July decision was very difficult, lauding the historic statement of late Saudi king Abdullah bin Abdel-Aziz to support Egypt in the face of any sanctions.
"Our success is not only the success of the millions who took to streets on 3 July, but it was the success of the Arab brothers who stood by Egypt and understood our needs," El-Sisi said.
Nine years later: A better place
The president added that over the past years he has exerted tremendous efforts and has not stopped explaining what is going on in Egypt honestly.
What Egypt has seen since 2011 affected everything, the president noted, stressing that he seeks to change the life of Egyptians for the better.
He said Egypt is a much different olace today compared to nine years ago.
On the LRT project, El-Sisi said it is part of the country's big plan to develop its infrastructure and transport sector at a cost of over EGP 1 trillion.
Ahead of the meeting with the media professionals, the president inaugurated the country's LRT that links the New Administrative Capital and Greater Cairo. The LRT is a sustainable means of green mass transportation that runs on electricity instead of diesel.
He stressed the importance of projects of this sort in a country the population of which increases by 2.5 million people annually, saying that without these projects the state would not be able to move forward.
The state is working towards a better future, he said, adding that throughout the past three years the country maintained its stability despite the global crises, facing all attempts to discredit it or sabotage its achievements.