The current study aimed at establishing pupils’ competency levels in Numeracy and Literacy (English and Kiswahili). Further, it aimed at finding out the personal, home-based and school-based factors that influence the learning outcomes of Class 3 pupils. It also sought to assess pupils’ levels of acquisition of life skills. One significant finding of the study is that there are disparities in pupil competency levels among counties. Further, boys performed better than girls in Numeracy while the girls performed better in Literacy. It was also notable that a high percentage of pupils had not mastered essential basic competencies in Literacy (English and Kiswahili). In particular, pupils were unable to arrange words in alphabetical order, meaning that they would not be able to use a dictionary.