The persistent poor performance of students in the Junior Secondary School Certificate Examination by Basic Science students is causing concern and poses a problem in subsequent learning of science related courses. This study investigated the impact of Process-Based Instruction on science skills acquisition, performance and retention among Basic Science students in Zaria Educational Zone, Kaduna, Nigeria. The research was quasi- experimental control group design that employed pre-test, post-test and post-posttest. The study population comprised 4,157 (2,615 males and 1,542 females) students from twenty five co-education schools. Two schools comprising 75 students (44 males and 31 females) were randomly selected for the study, one was randomly assigned as experimental group while the other served as control group. The experimental group was taught using PBI while the control group was taught by LM. Both groups underwent pre-test treatment and post-test. Two instruments were used for gathering data, Basic Science Performance Test (BSPT) with reliability co-efficient of r=0.76 and Science Process skills Acquisition Test (SPSAT) with reliability co-efficient of r=0.71. The data obtained were analyzed using t-test statistic at p≤0.05 level of significance. Findings revealed that students taught by PBIS performed better and retained Basic Science concept learnt than those taught by LM. There was also difference in the academic performance and process skills acquired by male and female students exposed to PBIS in favour of male. There was difference in observation, classification, measurement and experimentation skills in favour of female students while interpretation of Data was in favour of males. All the subjects however, performed the same in inferring skills. Among recommendation given was that PBIS be incorporated in science teacher training curriculum by the Ministry of Education in order to produce teachers who would handle PBIS technique effectively. Also PBIS should be introduced in the first year of the secondary schools as means to reduce the gender related differences in science process skills acquisition between male and female students in schools.