Tononoka Secondary School principal Mohammed Khamis was buried on Monday afternoon after succumbing to Covid-19 earlier in the day.
His death came days after the school was closed following reports of Covid-19 spread.
His deputy Benjamin Kitsao Nzaro confirmed his death on Monday.
Khamis had been admitted a Mombasa hospital since last week.
The teacher had been admitted at the Coast General Hospital for the past five days at the ICU.
He was buried at 3pm under Islamic rites.
Khamis was eulogised as humble.
A message that circulated on social media indicated, "It is with great sadness that I announce the death of Mohammed Khamis principal Tononoka secondary, after a short illness. The body will be laid to rest today at 3 pm at Kikowani Cemetery. May his soul RIP. Inshallah."
Learning in two secondary schools in Mombasa was last week suspended after 15 teachers tested positive for Covid-19.
Mombasa county commissioner Gilbert Kitiyo said 11 teachers from Tononoka High School and four others from Mama Ngina High School have tested positive for the virus.
Kitiyo said samples from teachers at Star of the Sea Secondary School were also taken after suspected cases were reported.
Both the Star of the Sea Secondary and Tononoka secondary schools have been closed.
Learning, however, went on at Mama Ngina High School despite the cases.
Mombasa County Public Health chief officer Pauline Oginga said the management of the Star of the Sea School had requested for samples to be taken for testing.
A circular from the management, dated October 19 and signed by headteacher A. Mulinge, said the school had been closed for fumigation.
Education CS George Magoha has since warned schools against further reopening, as 931 more people tested positive for Covid-19 on Sunday.
Speaking in Nairobi, Magoha said the Cabinet is yet to approve the decision to reopen for other grades.
“The government has not authorised the further reopening of other schools in public, private or international schools… that decision is yet to be considered by the Cabinet and when we get to it, the nation shall be told,” Magoha said.