Schools in Nyanza and Western performed well in the Kenya Certificate of Primary Education released on Tuesday by Education Cabinet Secretary Fred Matiang'i.
Kakamega, in Western, produced the nation's top performer with Kisii producing the best candidate in Nyanza.
Teachers and parents of St Anne Junior School Academy were in celebration after Goldalyn Kakuya, who has albinism, scored 455 out of 500 marks and top the class nationally.
Booker Academy, Mumias, also in the county, had Kasana Valerie Najjuma score 445 marks.
According to head teacher Tom Omuhaka, 40 out of 83 candidates scored over 400 marks.
"This is our second-best performance. In 2011, we had 63 candidates with over 400," Mr Omuhaka said.
Antulay Asif scored 436 marks and twins Talitha Rozally and Olive Wabwire 405.
Sarah Nyambori Onderi, 13, from Elsa Academy, Kisii, had the best score in Nyanza with 442 marks.
When the Nation visited the school, parents and teachers were celebrating the soft-spoken girl, who blamed sickness during the exams for not doing even better.
"I am very happy as I have seen that my dreams have started coming true," Nyambori, who said she wants to be a neurosurgeon, said.
Ms Elizabeth Orenge, the school's deputy director, said: "So far, we have 19 students who have scored above 400 marks." There were 68 candidates.
Ian Judah Obare topped Imperial Academy with 432 marks.
Judah said he wants to be an engineer. His schoolmate Sheila Moraa scored 425 marks and wants to be a doctor.
Kisii private schools continued their long reign at the summit.
At Set Hill Green Academy, Lucy Busuru, 13, scored 438 marks to be the top girl in the county.
Busuru, who said she wants to be an engineer, was the county's second-best candidate after an Elsa Academy boy scored 442 marks.
More than 25 candidates scored over 400 marks at Set Hill.
At Elimu Academy in Kisii town, Alex Omindeh 13, scored 431 marks, while at least two pupils at Excel Elementary in Ogembo scored over 400 marks.
Ann Mwita scored 404 to emerge the best in a class of 25 candidates.
Makini School, Kisumu, was celebrating producing the county's top candidate.
Gift Janet Achieng, 14, scored 439 to lead the school's pioneer KCPE class of 16 and top the county.
Last year, the county's top score was 433 marks.
Achieng said she expected to do well but being top was a surprise.
She was followed by Sonia Jani Alando (433 marks) of Aga Khan Primary and Tnicky Achieng Ndolo (432) of MM Shah Primary.
Golden Elite Academy director Charles Ochome said there was no cheating in the exam.
Government-run Moses Mudavadi Primary School, Mululu, maintained its record, producing the top candidate in Vihiga, Troon Amiani (441 marks).
Number two Philip Mangale (430), also from the school, tied with Wayne Philip of privately run Mudasa Academy.
"We have done well. Our candidates returned good marks," head teacher Kihima Eboso enthused.
At Hekima Academy, Mbale, Sophy Wanjiru lead with 401 marks while the last in the class scored 303 marks.
At perennial Nyamira leader Eronge SDA Boarding, the top candidate scored 431 marks, up from last year's 426.
Head teacher Kepha Bwana said Duncan Omweri led the pack of 189 ahead of Evascophia Oyaro (411), Claire Oywori (408), Edwin Kimuruai (404) and Joy Mang'oa (403).
Its academic rival, St Andrews Kagwa Boarding, had received results for only one candidate, Alex Mokaya. He scored 409 marks.
Homa Bay's top pupil was Leonard Ochieng' Pio from St Peter's Cape View Academy with 441 marks as 19 candidates scored over 400 marks.
Janeiro Junior Academy produced some of the top pupils in Homa Bay County with initial results indicating a mean score of 400.78 marks.
Out of 46 candidates, 23 got over 400 marks.
Oyugi Rosemary Akoth, 13, led with 431 marks.
Akoth said said she wants to be a lawyer and would like to join Kenya High School.
She was followed by Kisuge Neema Onyango (430).
"We had a mean score of 400 marks from last year's 378," head teacher Philip Aduda said.
Reports by Benson Amadala, Nyaboga Kiage, Derick Luvega, Henry Nyarora, Shaban Makokha, Victor Otieno, Victor Raballa, Magati Obebo, Barack Oduor, Gaitano Pessa, Nelcon Odhiambo, Rushdie Oudia, Elizabeth Ojina, Elisha Otieno, Viviere Nandiemo and Ruth Mbula