Two children were reported missing after a heavy downpour hit Laisamis, Marsabit county, on Thursday evening.
The boys aged 10 and 14 had been herding about 200 goats which were swept away by the raging waters, said the Kenya Red Cross Society.
Red Cross said via Twitter on Friday that a classroom collapsed in the area.
"Marsabit, Isiolo and Samburu are among the counties that received above average rainfall," Red Cross saod, adding floods and mud rendered road impassable.
In Turkana county, an unconfirmed number of families were affected.
A section of Kalokal-Lodwar road was cut off and Nakiria river broke its banks leading to flash floods, Red Cross said.
In Nairobi on Thursday, motorists and commuters were stuck in traffic following heavy rains that .
Several roads including Kenyatta Avenue, and Ojijo Road in Westlands were flooded, forcing pedestrians to wade through to get to different parts of the city.
The meteorological department had warned of heavy rains from April to June.
It said Coast, Western, Central and Rift Valley regions would be affected.
Red Cross said heavy rainfall of 50mm or more is expected at the Coast, Western, Central and Northeastern parts of the country.
