For many years, malaria has remained to be one of the global major causes of morbidity and mortality. Many efforts to address the epidemic have been introduced. In the recent years, the use of mobile phone as a tool for disease (malaria) surveillance has been gaining momentum. The mobile phone reporting introduced due to the delayed of malaria cases reporting and follow up which was contributed largely by the traditional system of manual reporting using hard copy on monthly basis. The general objective of this study was to examine factors affecting performance of MEEDS at Zanzibar Malaria Elimination Programme. The evaluation also explored causes which lead to un-time reporting, low awareness of community and follow up of malaria cases. The study used descriptive cross-sectional study design in which mixed method approach was employed to collect data. A total of 184 respondents were included in the study. Purposive sampling technique was used to select 27 study participants from 184 respondents. The data collection was done through interviews, focus group discussion, documentary review and semi structured questionnaires. Quantitative data were analyzed by using Stata software 13th version whereas; qualitative data were analyzed thematically through ATLAS.ti software .The consent forms were given to the participant’s prior data collection. The findings revealed that un-time reporting in MEEDS was influenced by inadequate training of health workers, un-functional working facilities, and inadequate staffs, lack of motivation, supervision and network problem. The study also found that delaying of follow up of malaria cases was due to low awareness of community, lack of health insurance for District Malaria Surveillance Officers, different of reporting system between public and private facilities, and delay of confirmation reports for both public and private facilities once data has been sent. The study recommends that, health workers be trained or gets refresher training, all health facilities be invited to attend feedback meeting, working facilities be replaced on time and BCC/IEC materials be developed to make people aware about MEEDS.