Background: Promoting Science and technology is one of main long term objectives and tasks of Rwanda. Promotion of Science and technology depends on mathematics worldwide. To know the level of students’ performance in Mathematics and how to improve it, the assessment of students in form of summative and formative is the best predictor of Academic achievement in Mathematics. This current study sets out to explore the effect of formative assessment tools on students’ academic achievement in Mathematics in Kayonza District. This research aimed at exploring the formative assessment tools that are currently used in teaching and learning mathematics, assessing the factors that influence secondary school learner’s low performance in mathematics and exploring the effects of formative assessment tools on secondary school students’ achievement in mathematics. Materials and Method: The study adopted a mixed research design using both qualitative and quantitative approaches. A sample size of 95 respondents were drawn from a target population of 1851, it was calculated using Slovin’s formula. Purposive, stratified and simple random sampling techniques were used to select 95 respondents from 1851. Questionnaire and Interview as well as documentary tools were used to collect both primary data. Data was cleaned, coded, entered and analyzed using Statistical Package for Social Science (SPSS, Version 21.0). Quantitative data was analyzed using frequencies, percentages, descriptive statistics (means and standard deviations) while Qualitative data was analyzed in narrative way. SPSS was used because it is fast and flexible and provides more accurate analysis resulting in dependable conclusions. Results: Quantitative findings revealed that coursework, teachers’ observations, group/class work and test assignments were used by the teachers at in secondary schools at Kayonza District. However, the results showed that teacher respondents agreed that fear towards mathematics (strong mean of 4.29), high number of students per classroom (mean= 3.98) and low level of teachers’ training (Mean=4.99) as well as lack of science culture among students (Mean= 3.78) were the leading factors to low performance in mathematics in secondary schools in Kayonza District. The study findings further indicated use of group discussions to enhance students’ enactment and scoring, student’s participation in mathematics duties/tasks through observations and group work encourages peer learning affect positively the students; performance in Mathematics in Kayonza District. Using Pearson correlation coefficient, the results revealed that one-unit increment in using formative assessment tool led to 0.791 increase in learners’ academic performance in mathematics in 12 secondary schools in Kayonza District. Conclusion: In line with the findings and the conclusions emerging from the study, the following recommendations are made to the teachers, school staff and District as well as Ministry of Education (MINEDUC): Teachers should therefore plan carefully for mathematics quizzes, homework and end term mathematics tests to increase students’ motivation to learn mathematics. In addition, it is recommended to the school staff, the district and MINEDUC to evaluate teachers regularly because evaluation is an obvious vehicle for using incentives to direct the teachers on the path towards professional growth and improvement