Malaria is a life threatening infectious disease that constitutes a major global public health and economic concern. Consequently, the WHO has recommended a T3 initiative (Test, Treat & Track) to help curb the scourge globally. This study aimed to ascertain the efficacy of malaria diagnosis in malaria case management and perception of community pharmacists on the WHO recommended standard of parasitological diagnosis before commencement of treatment within Abuja metropolis. A descriptive cross sectional study was performed amongst 207 community pharmacists within Abuja Metropolis. Data was obtained through structured, self-administered questionnaire. The association of respondent characteristics with the awareness, practice, and perception of malaria testing, and treatment was evaluated by Chi-square analysis for proportion. Where the number of categories was less than five, Fisher exact test was used. Seventy-two percent (72.9%) were aware of the WHO recommended T3 initiative on malaria case management. However, less than 10% of respondents had training in all the three components. On practice, 28.5% of community pharmacists carry out malaria diagnosis with a confirmatory test before instituting treatment. Ninety-two percent (92.3%) treat malaria based on clinical signs and symptoms only. Despite the high rate of clinical diagnosis, a majority (84.1%) agreed that the confirmatory test is more effective and efficient in malaria case management than clinical diagnosis. Most respondents (60.4%) reported that the confirmatory test most readily available was mRDT. Eighty-seven percent (87%) have good perception on parasitological confirmatory testing for malaria diagnosis and most respondents have confidence in results from the malaria confirmatory test while 68.6% trust their malaria confirmatory test skill. A little above half (52.7%) of the respondents treat for malaria regardless of negative confirmatory test results when the patient insists on treatment. A higher proportion (39%) of male community Pharmacists compared to females carry out malaria diagnosis with a confirmatory test before treatment. There was significant association of perception on the efficacy of a parasitological confirmatory test for malaria with age and work experience and there was significant association of work experience with the practice of confirmatory testing before treatment (P<0.05). Inferentially, this is call to action for government, professional bodies in the health sector and all committed to fight the scourge of malaria for more awareness to the general public on importance of the WHO T3 and capacity strengthening for the frontline health workers -community pharmacy attending to community needs on malaria case management.