While in Cairo Fourier helped found the Cairo Institute and was one of the twelve members of the mathematics division, the others included Monge, Malus and Napoleon himself. Fourier was elected secretary to the Institute, a position he continued to hold during the entire French occupation of Egypt. Fourier was also put in charge of collating the scientific and literary discoveries made during the time in Egypt.
Habang sa Cairo Fourier tumulong na natagpuan sa Cairo Institute at noon ay isa sa mga labindalawang kasapi ng dibisyon ng matematika, ang iba kasama Monge, Malus at Napoleon kanyang sarili. Fourier ay elected secretary sa Institute, isang posisyon na siya ang patuloy na humawak sa panahon ng buong French trabaho ng Ehipto. Fourier ay din ilagay sa singil ng collating ang pang-agham at pampanitikan discoveries ginawa sa panahon ng oras sa Ehipto.