Influenza seasonality in equatorial countries is little understood. Seasonal and alert influenza thresholds were determined for Malaysia, using laboratory-based data obtained from the Malaysia Influenza Surveillance System and a major teaching hospital, for 2011-2016. Influenza was present year-round, with no clear annual seasons. Variable periods of higher transmission occurred inconsistently, in November-December, January-March, July-September, or a combination of these. These coincide with seasons in nearby southeast Asian countries or winter seasons of the northern and southern hemispheres. Changes in predominant circulating influenza type were only sometimes associated with increased transmission. The data can inform public health interventions such as vaccines. This article is protected by copyright. All rights reserved.