Research into private distance education sector, particularly on student support system, is very rare in Ethiopian context. The purpose of this study, therefore, was to investigate the practice and challenges of learner support system in Ethiopian private distance education institutions in case of Alpha University College Gondar Branch. To this end, mixed research approach was used. From the total of 253 populations (male=132 and female= 121), 134 (male=68 female=66) sample participants were selected through available sampling technique. Comprehensive sampling was employed to select center staffs in Alpha University College Gondar Branch. The relevant data were collected through questionnaire, document analysis and semi-structured interview. The quantitative data were analyzed using descriptive statistics (frequency, percentage, mean and standard deviation) and inferential statistics (one sample ttest, independent samples t- test and one way ANOVA) whereas; the qualitative data were analyzed through verbal description. Based on the analysis, it was found that learner support service was not implemented in the expected manner and the learners were dissatisfied by the services which were delivered by the institution. That is, the implementation of learner support was minimum and not properly practiced. Appropriate feedback was not provided and various modes of delivery were not used in the implementation. It was also found that the practice of learner support was challenged by many factors of which individual related challenges including expensiveness of communication and travel, work overload of learners, employers challenge to give leave and conflicting commitments of learners; institutional related challenges including lack of resources and low commitment of the institution to deliver effective learner support service and instructional related challenges including inadequate content of instructional materials and insufficient knowledge of tutors were the most serious ones. Based on those findings, the institution were not able to implement effective learner support service and challenges were not taken by the concerned bodies. Hence, some recommendations were forwarded as a solution for the identified problems.