Learning institutions are likely to remain closed for the better part of the year, keeping more than 18 million at home, if projections of how the coronavirus may spread come true.
This may disrupt the school calendar and result in learners retaking lessons of the classes they are in when the pandemic is finally brought under control.
As of Thursday evening, the country had 110 confirmed Covid-19 cases but a Ministry of Health model shows the numbers are expected to hit 1,000 by the end of the week, 5,000 by mid-month and 10,000 by the end of April.
Three weeks of first term have already been wasted, with the schools having been scheduled to close next week.
By next week, stricter restrictions on movement may be in place as learners remain at home.
With the figures expected to rise due to community transmissions, much of the second term will be eaten away and preparations for end of year national examinations hampered.
When President Uhuru Kenyatta suspended learning on March 15, Kenya had only one case of the deadly virus that has resulted in more than 1.5 billion learners worldwide remaining at home.
It was one of the major measures imposed to contain the virus and potentially remains one of the last to be lifted.
Schools and colleges are considered high-risk areas because of the many learners they hold, and who come from different backgrounds.
Though the government is silent on any possible reopening, there are indications that there are preparations for the closure taking a longer time than originally anticipated.
Officials at the Education ministry declined to comment as all matters concerning the coronavirus outbreak are being communicated through Health CS Mutahi Kagwe's office.
On Monday, Deputy President William Ruto announced that the government had directed the Education ministry to work with county governments to identify at least 20 boarding schools per county that can be converted into health facilities and isolation centres, if the need arises.
"The health ministry will work with governors to ensure it is done ASAP," Dr Ruto posted on his Twitter handle.
On the same day, Mr Kagwe said the government will utilise all available resources at its disposal to contain the spread of the coronavirus disease.
"Everything remains on the table. We are seeing other countries putting up stadiums. We have boarding schools which can take up to three hundred thousand capacity. This is our advantage. There are airport hangars too and if it is necessary, we shall activate them," Mr Kagwe said.
At the time of the closure, chair of the Kenya Secondary Schools Heads Association Kahi Indimuli was hopeful the it would not take long.
"It won't be much if schools re-open in 30 days, we can then adjust the school calendar. If not, as a sector, we'll have to re-organise and plan for national examinations and synchronise our calendar with that of the universities," he said.
But on Wednesday, the Kenya Union of Post Primary Education Teachers chairman Akello Misori called for the postponement of the KCPE and KCPE exams, citing anxiety in schools.
The preparations for the exams are further complicated by the fact that the tests are printed in the UK, which is currently under lockdown.
There were more than 29,400 confirmed Covid-19 in the UK cases by and over 2,300 coronavirus-related deaths.
The government ordered the closure of schools and cancellation of GCSE and A-level examinations on March 18.
The Kenya National Examinations Council timetable has KCPE tests starting on October 27 while the KCSE theory exams are to start on November 2.
Also disrupted are schools co-curricular activities, some of which were already at the regional level.
Mr Indimuli suggested that some of them be combined (at national level) with Term II activities.
If the closure takes more than five months, private schools will particularly feel the pinch as they mainly depend on school fees for their running.
Many will struggle to pay teachers and other workers.
The Bridge International Academies have already sent their teachers home and told their staff to consider the move as "temporary lay-off" owing to the inactivity at schools.
The chair of the Kenya Primary School Heads Association, Nicholas Gathemia on Thursday said that there was "total engagement with the Ministry of Education" over measures to protect school children from coronavirus disease.
He said that closing schools was the best decision the government could make as safety of the learners overrides everything else.
There are about 13 million learners in public and private primary schools in Kenya.
"We're happy because the children are now safe in their homes. Now we need to sensitise the parents not panic and keep their children at home until it is declared safe for them to come back to school," he told the Nation on phone.
The unexpected closure has presented challenges for parents, learners, teachers and authorities as they grapple with the interrupted learning.
Many parents were unprepared for distance and homeschooling and are now struggling to help their children with schoolwork.
Though homeschooling is encouraged, the absence from school has denied nutrition to thousands of Kenyan children who benefit from school feeding programmes.
Parents who had not budgeted to feed the children during the period they would have been in school (including the ones in boarding schools) will now have to dig deeper into their pockets.
While the Kenya Institute of Curriculum Development has stepped up its virtual learning output through radio and TV lessons and the Kenya Education Cloud, unequal access to the digital learning tools leaves out thousands of children, especially in the marginalised areas and the urban poor.
Virtual learning at a number of upscale private schools is also ongoing, leaving thousands of learners in public schools at a disadvantage.
The prolonged closure raises concern that dropout rates might go up, especially among vulnerable communities.
These include the pastoral and nomadic communities and also the urban poor where early pregnancies and child labour are prevalent.