During his third successive year in attendance at a Coptic Christmas Mass at Cairo's St Mark's Cathedral in the Abbasia district, Sisi said that he had already donated EGP 100,000 towards the project.
He said he intended construction of the mosque and church to be completed by 2018.
Their construction, said Sisi, would coincide with the 50 year anniversary of the construction of St Mark's Cathedral, the scene of a deadly bomb attack in December that left 25 people dead.
During his address on Friday, Sisi also reiterated a previous commitment to rebuild all churches that were damaged or destroyed during the tumultuous period that followed the overthrow of former President Mohamed Morsi in a military coup that brought Sisi to power.
Standing with Coptic Pope Tawadros II Sisi said that two remaining churches were awaiting rehabilitation, one in Minya, the other in al-Arish, vowing that work on the two churches would be completed in the coming weeks.
The Egyptian Initiative for Personal Rights has recorded at least 77 attacks on Coptic Christians between 2011 and 2016 in Minya, a governorate south of Cairo containing at least a third of Egypt's Christian population.
Copts make up around 10 percent of Egypt's population of 90 million and celebrate Christmas on 7 January.
In recent months, Egypt has witnessed a rise in violence against Coptic Christians, which some have connected to a rise in violent acts committed by Islamic State group militants in the North Sinai.
Speaking from St Mark's Sisi sought to downplay divisions and animosity towards Copts in Egyptian society, stating "We are all one".
"Egypt, God willing, will see light from us all to teach people [across the world] love, peace, security and prosperity," said Sisi, rebuking criticism of his attendance of a Christmas service.
"I am here in a house of God, and I say please God, keep Egypt safe."
In 2015, Sisi became the first Egyptian president to attend a Christmas Mass.
At a time when Egypt's economy is in dire straits with the pound having fallen to over 16 per $1 on the black market last year, it remains unclear where Sisi will raise the funds for his momentous contruction plans.
The Egyptian president is no stranger to grandiose statements. In 2015 he vowed to construct a new Egyptian capital east of Cairo before plans were suspended last year.
Speaking in May last year he also vowed to eliminate all of Cairo's slums within two years, a hugely ambitious project, perhaps not matched by his government's coffers.