This study examined the use of the set, area, and linear models of fraction representation to enhance elementary pupils’ conceptual understanding of fractions. Pupils’ preferences regarding the set, area, and linear models of fractions during independent work was also investigated. This study took place in grade eight “A class” consisting of 43 pupils in Hai- Negeil primary school in Juba county Central Equatoria State. Pupils participated in classroom activities which required them to use manipulatives to represent fractions using the set, area, and linear models. Pupils also had experiences in using the models to investigate equivalent fractions, compare fractions, and perform operations on fractions especially Addition and Subtraction. Mixed method approach was used in this study. Data collection instruments used were an observation schedule which was collated by the researcher in teaching the lessons for the period of three weeks, Pupils maintained their work sheets or journals throughout the study; they completed pre and post assessments, participated in class discussions and 20 out of 43 pupils were randomly selected for interviews concerning their fraction model preference. Data were analyzed using inference statistics (one sample t-test was used) and the results for the onesample statistics showed the means of pretest= 19.77and posttest = 33.70, t-value for pretest = 17.43, for posttest = 40.33 and p-values are all 0.000 and the .The mean improvement was 14.14 and an increased in conceptual understanding ranged from 7 to 26 points and some pupils showed more growth through other methods of data collection. Finally, the data collected from pupils confirmed that the uses of manipulatives indeed have value in the teaching of fraction concepts and operations, especially addition and subtraction of fractions. The data concerning student preferences were inconsistent, as pupils’ choices during independent work did not always reflect the preferences indicated in the interviews. Therefore, teachers are highly recommended to plan and continue to incorporate activities that should involve the uses of set, area, and linear models of fraction representation. They should also plan to provide more opportunities to discuss solving fraction problems in context and how to use the context of the problem to help determine which model of fraction representation would be most useful.