Background: Cardiopulmonary bypass (CPB) is associated with increased fluid accumulation in body and ultrafiltration is a method used to decrease body fluid volume and tissue oedema as the consequences of haemodilution after cardiac surgery with CPB. This study aimed to compare the effects of modified ultrafiltration (MUF) versus combined conventional ultrafiltration (CUF) and modified ultrafiltration on the duration of mechanical ventilation and hemodynamic status in paediatric patients undergoing congenital heart surgery. Materials and Methods: A simple randomised clinical trial was conducted on eighty paediatric patients undergoing congenital heart surgery on cardiopulmonary bypass. Patient management was standardised, and intensive care staff were blinded to group allocation. Preoperative Aristotle comprehensive complexity level, ultrafiltrate volumes, perioperative haemodynamic data, haematocrit, Transesophageal echocardiographically (TEE) determined ejection fraction (EF), fractional area change (FAC), temperature drift, arterial oxygenation, time of extubation, ventilation, comparison of inotropic drugs, postoperative chest tube drainage, intensive care unit (ICU) and hospital stay were recorded in CUF and CUF plus MUF. Results: There was no operative mortality. Technical difficulties prevented completion of modified ultrafiltration in 3 patients of 40 in CUF+MUF. In this study there were 33.75% females and 66.25% males with a median age 441 days, mean weight 10.19 kg and Aristotle comprehensive complexity score level-2. CUF+MUF had greater ultrafiltrate volume (883 ± 82.7 ml; (p = 0.014). Duration of ventilatory support was 103.2±25.85 hours versus 61.4±13.74 hours in CUF and CUF+MUF respectively, (p= 0.004). Chest tube drainage in the first 48 hours was (107.63±23.83 and 79.31±47 ml) in CUF and CUF+MUF respectively, (p= 0.003). Inotropic infusion requirement was significantly less in CUF+MUF compared to CUF. EF and FAC were 10 % and 4 % higher at 45 minute