Science Process Skills acquisition is the foundation for the effective learning of science even at the primary or basic level of education. The acquisition of Science Process Skills helps the learner to perceive the relevance of science in everyday life. The purpose of the study therefore was to investigate Gender and Acquisition of science process skills among junior secondary school (JSS) 3 students in Calabar Municipality and the implication for implementation of Universal Basic Education objectives. One research question and two hypotheses were used for the study. Two hundred (200) JSS 3 students in three (3) co-educational schools participated in the study. A Science Process Skills acquisition (ASPA) test developed by the researchers was used for data collection. Descriptive statistics in terms of percentages was used to answer the research question, independent t-test and contingency chi-square were used to test the null hypotheses at (p<0.05). The result of analysis showed that majority of the students acquired the basic Science Process Skills measured but at a very low and little above average, students who acquired Science Process Skills performed better than those who didn’t acquire those skills measured and gender did not significantly influence the acquisition of Science Process Skills at the upper basic level of UBE. Based on the findings, it was recommended among others that students in the UBE scheme should be actively involved in classroom activities, and that activity-based methods of instruction be employed in teaching Basic sciences to enable a greater percentage of students to acquire Science Process Skills with higher scores for effective learning of Science subjects.