"These claims only exist in the imagination of those who promote them," the foreign ministry said in the statement.
On Thursday, the Lebanese newspaper As-Safir said that 18 Egyptian air force pilots had been deployed on a military base in the Syrian central province of Hama.
It added, however, that it was "unclear" whether they were taking part in any military operations.
Sisi, the former army chief who was elected president in 2014, expressed support for the Syrian military during an interview aired Tuesday with Portuguese broadcaster RTP.
Asked by the interviewer whether he meant the Syrian military, Sisi, who has overseen a warming of ties with Syrian President Bashar al-Assad's main he responded: "Yes."
Syrian security services chief Ali Mamluk made a surprise visit to Cairo in October and met Egyptian officials, in his first public foreign visit in five years.
Sisi, who was elected in 2014 almost a year after overthrowing his Islamist predecessor Mohamed Morsi, has cracked down on Islamists and is battling a deadly jihadist insurgency.
Saudi Arabia backs rebels trying to oust Assad, while Russia and Iran are supporting him militarily.
Saudi Arabia suspended oil shipments to Egypt in October, a move announced after Cairo backed a Russian-drafted resolution on Syria in the UN Security Council, angering Riyadh.
And while Egypt has on paper been part of a Saudi-led Arab coalition in Yemen backing pro-government forces against Shiite Huthi rebels, analysts say that behind the scenes, Egypt has been reluctant to engage.
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