Cynthia Auma, a candidate at Ndhiwa primary school, failed to appear during day two of the national exams.
She wrote the exam administered on day one of the national tests which began countrywide on Tuesday.
Nobody knew her whereabouts since she was neither at home nor in school.
The girl allegedly left home on Tuesday night and never returned.
Homa Bay county police commander Marius Tum said the girl's parents looked for her in vain.
"The parents went to look for her in school in the morning but they did not find her," Tum said on Wednesday.
The police boss said they had launched investigations to ascertain the minor's whereabouts.
"Preliminary investigations reveal that girl must have eloped with a man. But we are digging deeper."
Ndhiwa sub-county director of education Maurice Jayoro said two cases of absenteeism were reported in the region.
"There was a case where two candidates missed day one papers. I will find out if this girl is part of the two cases or not."
-ROBERT OMOLLO