In an attempt to curtail examination malpractice, the Joint Admission and Matriculation Board (JAMB) has been generating different paper types with a different order of test items in the Unified Tertiary Matriculation Examination (UTME). However, the permutation of test items may compromise students’ performance unintentionally because constructive suggestions in theory and practice recommend that test items be sequenced in ascending order of difficulty. This study used data collected from a random sample of 1,226 SSIII students to ascertain whether the permutation of test items has any effect on the performance of students in two different subjects (Use of English and Mathematics). The study adopted the Equivalent Groups Quasi-Experimental Research Design with three independent groups. Findings emerged, amongst others, that there is a significant difference in the performance scores of prospective university students’ in use of English and Mathematics examintaions arranged in three different orders (ED, DE, R). There are no significant gender differences in the performance of students in Use of English and Mathematics based on test item permutation. However female students perform better than male students when test items are arranged in ascending order of difficulty while males perform better when test items are arranged in descending order of difficulty. It was concluded that the permutation of test items in UTME examination tends to affect the performance of students in Use of English and Mathematics. This finding has implications for the future conduct of UTME examinations and enrolment into higher education as the randomization of UTME test items changes the difficulty order of different paper types. It was recommended that other measures of curtailing examination malpractices that would not affect students’ academic performance should be adopted.