Malaria remains a significant public health problem in tropical countries, including Indonesia. According to the World Health Organization (WHO) report in 2021, there were approximately 229 million malaria cases and 409,000 deaths worldwide in 2019. In Indonesia, malaria remains endemic in several regions, including the Tanimbar Islands Regency, where tropical environmental conditions support the breeding of Anopheles mosquitoes as the primary vector. This study aimed to evaluate diagnostic methods and therapeutic outcomes among malaria patients in this region. The study employed a cross-sectional design with a total sample size of 200 respondents (n = 200). Statistical analysis was conducted using the McNemar test and chi-square test.The results showed that the majority of respondents were female, aged 15–49 years (71%). Based on occupation, malaria cases were most commonly found among individuals in informal sectors such as fishermen, farmers, and laborers (33.5%), with most respondents having a senior high school level of education (54.5%). The predominant infection was caused by Plasmodium vivax, with most patients exhibiting moderate levels of parasitemia. Most patients achieved recovery after receiving treatment. Statistical analysis indicated a significant difference between Rapid Diagnostic Test (RDT) and microscopic examination methods in malaria diagnosis. Furthermore, there was a significant association between the diagnostic methods used and patients’ therapeutic outcomes (p < 0.05), as well as between parasitemia levels and RDT results in determining the effectiveness of malaria diagnosis.