Thirteen years port sampling data (2005-2017) in the gillnet fishery of Sri Lanka was used to analyze the catch rates of skipjack tuna. Skipjack tuna is the main target species in the gillnet fishery. All gillnet catches including the catches made by popular gear combinations operate in gillnet fishery (gillnet–longline, gillnet-handline and gillnet-ringnet) were considered for this study. Five vessel types which were operated during this period in the tuna fishery of Sri Lanka have caught skipjack tuna. Fish landing data and biological data of key species in gillnet fishery are collected during the port sampling. Accordingly, the unloaded skipjack tuna catches made by the vessels are recorded and these data with other data relating to fishing operations are also recorded and entered into the national database (PELAGOS). Year, month, boat type, gear/ type, trip duration (in days) and number of net panels used for fishing operation were considered for this analysis. A monthly series of skipjack tuna Catch Per Unit Effort (CPUE) in terms of catch in kg per boat per trip was derived from the catch data. A Gamma based Generalized Linear Model (GLM) was fitted to determine the relationship between the explanatory variables and monthly average CPUE. All zero-catch rates of skipjack tuna were excluded for the analysis. All main effects and their first order interactions were taken into consideration. The fitted GLM model explains 83.8% of the deviance and the vessel type was found to be the most significant factor for determining the catch rates of skipjack tuna. Among the first order interactions, year : month was found to be the key explanatory variable. The fitted GLM model comprises of main effects only explains 65.5% of the deviance.