Prolonged pleural effusion is a fairly common condition which has considerable impact on complicated and longer hospital stays after Fontan surgery. Identifying the patient population prone to have pleural effusions is still seeking for an answer. This study is to determine the variables that may predict prolonged pleural effusion according to the data of 69 patients who underwent Fontan operation between June 2018 and December 2020 and survived to date. Prolonged pleural effusion was defined as the need for a chest tube for more than 7 days. Two patient groups, with and without prolonged effusion, were compared in terms of pre-, peri-, and post-operative variables. The patients were subdivided into "high-risk" and "low-risk" groups based on the pre-operative catheterisation data. The most frequent main diagnosis was tricuspid atresia (n: 13, 19%). Among 69 patients, 28 (40%) had prolonged pleural effusion whereas 11 (16%) had effusions that lasted longer than 14 days. Ten patients among prolonged effusion group (35%) had pulmonary atresia coexistent with the main diagnosis. Fontan operation was performed in 6 patients (8.7%) over the age of 10, and 4 of these patients (67%) had prolonged pleural effusion. Among numerous variables, statistical significance between the two groups was achieved in pre-operative mean pulmonary artery pressure, post-operative albumin, C-reactive protein levels, length of hospital stay, duration of chest tube drainage, and amount of effusion per day. Early recognition and treatment strategies with routine medical protocol use remain to be the cornerstone for the management of post-operative prolonged pleural effusions after Fontan surgery.