The departing British prime minister and Mr El Sisi also talked about the creation of the UK-Egypt Investment Council and new investment opportunities in Egypt.
The countries' close defence and security relationship was praised by Mr Johnson and Mr El Sisi, Downing Street said.
Mr Johnson thanked Mr El Sisi for his role in helping to get grain out of Ukraine’s ports and on its way to countries facing desperate food shortages as a result of Russia’s blockade.
Cop26 Environment Ministers - in pictures
The leaders looked ahead to the UK handing over the Cop Presidency to Egypt at Cop27 in November, Downing Street said.
They also agreed on the importance of driving forward the transformative action on climate change agreed to in Glasgow last year.