The purpose of this study was to investigate pupils‘ understanding and interpretation of the equal sign and variables, so that instructional resources could be identified to improve student‘s conceptual understanding about mathematical equivalence. A designed-based research, using mixed method, was conducted in a selected primary school in Juba, South Sudan. An assessment test comprising 4 question items was administered to 31 Grade 8 pupils. Data collection was done by using pre and post test, audio recording, observations, and pupils‘ journals.Thereafter, six pupils were purposively selected based on their responses in the pretest, signifying possible misconceptions regarding the equal sign to participate in FGD.The data for assessment was analyzed using SPSS by Paired Samples t test. The researcher also reviewed the Mathematics textbooks for the presentation of equal sign concept and equation types. The results of the test indicated that a significant number of Grade 8 pupils could not describe the meaning of the equal sign correctly. The study also revealed that some Grade 8 pupils in this school interpreted the equal sign as a ‗do something‘.There is a cognitive gap between arithmetic and algebra. There was a significant improvement after PI. Mathematics textbooks (grades 6, 7 & 8) presented equal sign in standard operations-equals-answer contexts (e.g., 6 + 3 = 9) and was rarely presented in nonstandard operations on both sides contexts (e.g., 6 + 3 = 4 + 5).The researcher described the essential elements of instruction that advanced equal sign understanding. Teachers should focus on the meaning of the equal sign and equation structure on a regular basis and not assume that the symbol is well understood. This finding is an eye-opener for restructuring the mathematics curriculum to meet the pupils‘ needs. Further research is requisite for larger sample size and multiple schools.