The study examined the effects of flipped classroom learning on perception in genetics concepts among secondary school students in Gusau, Zamfara State, Nigeria. The research design employed was quasi-experimental; specifically, pre-test, post test, non equivalent control group design. A sample of 279 SS 3 Biology students drawn using multistage sampling technique from 5,804 SS 3 students for 2020/2021 session from 29 senior secondary schools in Gusau Local Government Area, Zamfara State, Nigeria. Students’ Perception of Genetics Concepts Scale (SPGCS) was the instrument used in collecting data, as Pretest and Post-test. A reliability coefficient of 0.98 was found using Cronbach’s alpha. The data were analysed using mean, standard deviation and Independence Z-test at 0.05 level of significance. Results indicated that students taught using Flipped Classroom Learning possessed high level of perception in genetic concepts than those exposed to lecture method with significant difference in the mean perception scores. The findings equally indicated the insignificant difference between the perception of male and female students exposed to Flipped Classroom Learning. The study recommends among others that Biology teachers should be encouraged to use Flipped Classroom Learning as the main teaching strategy to improve students’ perception in genetics concepts in senior secondary schools. Similarly, Biology teachers should be trained by the Ministry of Education and other education agencies on effective procedures for implementing Flipped Classroom Learning for high level of perception in genetics concepts.