Malaria is a life-threatening parasitic disease caused by a protozoan of the genus Plasmodium and is one of the most important parasitic diseases of man globally especially in sub-Saharan Africa. This research was done to assess malaria infection and its relationship with the knowledge, attitude, perception and prevention among students of boarding schools in Gboko Local Government Area. Five boarding schools within Gboko Local Government were selected for the study. A total of 370 students. Malaria in the schools was determined through malaria test via the examination of stained thick blood smears under the microscope. Structured questionnaires were administered to the participants to get information pertaining to their demography, knowledge, attitude, perception and preventive methods towards malaria. Thick blood films were stained using Romanowsky Field Stains. Chi-square was used for comparing infections and to determine the significant relationships at 95% level of significance. The results showed an overall prevalence of 20.8%. The prevalence of malaria was higher among female students (22.3%) than in male students (19.5%). Malaria was found most (10.8%) among students who use insecticide treated nets (ITNs). This study revealed that the knowledge and ownership of insecticide treated net (ITN) was high (86.2%) among the students. However, only 60.0% of the ITN owners actually use it. Thirteen percent of the students have phobia for the use of ITN while many students do not use the ITN for diverse perceived reasons. The treatment seeking behavior of the students showed that majority of the students (84.9%) access the school clinic when they have fever. This study has revealed that there are misconceptions on the knowledge of malaria among students and these are some of the factors leading to the risk and exposure of students to the bites of mosquitoes. The perceived beliefs on malaria in this study have no scientific basis and can easily be overcome through proper health education. Providing a mosquito free environment and promoting ITN usage as well as use of mosquito repellent cream among boarding school students may help achieve the desired protection against mosquito bites and subsequently prevent malaria.