The Form One selection has been met with national outcry after it emerged that many pupils had been placed in secondary schools they never chose.
In Kwale County, all Bethany Christian Academy pupils missed out on their choice schools.
The school was second best in the Kenya Certificate of Primary Education examination nationally with a mean mark of 417.
It closely followed Fred's Academy in Meru whose mean was 419.
The 15 pupils, their parents and the school now want to be told the criterion used in placing them in schools they never selected.
Ruth Chaka, the third best pupil in the country and top at the Coast with 446 marks, will not join Alliance Girls High School.
She has instead been selected to join Mama Ngina Girls Secondary School in Mombasa.
"I feel bad for being denied an opportunity to be in my dream school," she said yesterday, adding that the Ministry of Education should revisit the process of placing learners in secondary schools.
Another disappointed pupil is Lucy Nyarumba who scored 435 marks. Like Chaka, her dream school was Alliance Girls.
"I have also been selected to join Mama Ngina Girls. It is really heartbreaking," she said.
Baraka Rimba who had 434 marks wanted to join Mangu High School in Thika.
"I have just learnt that I am supposed to go to Friends School Kamusinga," the boy said, adding that he hoped the selection method would be reviewed.
Bethany Christian Academy director Young Lee said the selection was unfair "since it denies deserving children a chance to join the schools they only dreamt of".
Mr Lee added that the pupils dreams had been shattered, adding that it could affect their performance in future.
A pupil who sat the examination in Machakos County is expected to join Bartolimo Secondary School in Baringo County.
A candidate from Kilifi County will join Eregi Girls High School in Vihiga County while one from Kiambu will join a school in Wajir County.
Meanwhile, Valentine Karikonyi who sat the examination at Kitale Academy and scored 402 marks was happy to be admitted to Limuru Girls High School while her brother Allen Valentine Barasa who got 382 marks at Blue Hills Academy Ruai is to join Butere Boys High School.
Basic Education Director General Robert Masese could not be reached for comment.
While launching the selection to secondary schools last week, Education Cabinet Secretary Fred Matiang'i said the Ministry would ensure equity in placement in national schools by applying sub-county quotas, based on candidature strength and affirmative action where sub-county candidacy would be too low to attract a quota.
"By design, affirmative action aims to guarantee the participation of minorities and marginalised groups in national schools as clearly guided by the constitution," the minister told the teachers and other officials gathered for selection at the Kenya Institute of Curriculum Development, Nairobi.
At the same time, selection to county secondary schools begins across the country tomorrow.
Sub-county selection will be concluded by sub-county directors of education on Monday next week.