The focus of this study was to determine perception of examination malpractice and academic performance in Primary Science among sixth grade in Cross River State, Nigeria. In order to achieve the set objectives of this study, three hypotheses were formulated and tested. Two instruments were used for data collection. They were perception of examination malpractice questionnaire (PEMQ) and a 50-item primary science achievement test. These instruments were validated and administered to one thousand eight hundred and eighteen (1818) pupils out of sixty-eight thousand, two hundred and one (68,201) pupils in seventy (70) schools in the study population. A proportionate stratified random sampling technique was adopted hence; the study area was stratified into three educational zones with different populations. The data obtained were analyzed using Pearson Product Moment Correlation Coefficient (r), One-way Analysis of Variance (ANOVA) and Independent t-test statistical tests at 0.05 level of significance. The major finding of this study was that there was a significant relationship between pupil's perception of examination malpractice and academic performance in primary science. Based on the findings, it was concluded that if pupils understand the damage examination malpractice does to the educational system and study adequately; it will help them to perform well in science and minimize examination malpractice. It was recommended that pupils should be made to understand the dangers of examination malpractice and culprits caught in examination should be used to set good examples for others to enable them model adequate behaviours and study hard for their examination.