Two candidates tied at the top with 453 marks out of 500 in the tests carried out in three days.
In the 2018 KCPE exams, 527,294 were boys while there were 525,070 female candidates.
CS Amina noted that the performance had improved, with female candidates performing better than males in English, Kiswahili and Kenya sign language.
Male candidates performed better than the female candidates in Mathematics, Science, Social studies and religious studies.
There were 12,273 candidates with more than 400 marks in this year's exams. This, CS Amina noted, was a 1.17 per cent increase from the 9,846 in 2017.
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She also observed that more than half of the 2018 KCPE candidates scored more than 250 marks.
The number of pupils who scored less than 100 marks dropped to 2,177 candidates in the 2018 examinations.
Among candidates with special needs, the best out of the 2,495 candidates this year scored 446 marks. This marked an improvement from the 2017 performance in this category.
In 2017 there were 2,038 special needs candidates. The best candidate obtained 426 marks in the special exams.
The ministry had directed for a 100 per cent transition rate to secondary school. The candidates shall be issued with their admission letters before the commencement of the Christmas celebrations.
"It is a directive by President Kenyatta that all the candidates break for Chrismas while knowing the schools they have been selected to...There will be only selection, we will do it once and it shall be done well," stated CS Amina.
The selection process shall kick off on Monday, December 3, 2018. Individual results can be accessed by a candidate by sending their index numbers via SMS to 20076.