Abstract Background Cardiac microvascular obstruction (MVO) is a frequent injury of the myocardial microcirculation after successful recanalisation of the occluded coronary artery in myocardial infarction. At least in part, MVO is caused by embolised microthrombi of less than 200 µm diameter [1]. MVO leads to hypoperfusion of the myocardium and negatively affects patient outcomes. However, there is no effective treatment for MVO [2, 3]. Thrombolytic drugs are a promising approach, but they are difficult to deliver to the MVO area, and an increased risk of bleeding limits their use. In a previous study using an in vitro fluidic multi-scale model for MVO [4, 5], it was shown that controlled flow infusion (CFI) with a novel drug-delivering catheter could be used to effectively deliver highly concentrated intracoronary microdoses of a thrombolytic drug to the MVO area [6]. We now aim to investigate how such locally administered drug microdoses can induce thrombolysis as a possible therapeutic approach for MVO treatment. Methods A microfluidic chip (Fig.1) was used to study thrombolysis under flow using different microdoses of the thrombolytic drug alteplase. The chip consists of a tapered straight channel, which traps injected porcine microthrombi without causing complete channel occlusion (Fig. 1A). To mimic intracoronary CFI (consisting of temporary balloon occlusion of a coronary vessel for 90 seconds while drug is injected distally through a catheter) in vitro, microthrombi were incubated (without flow) directly in the chip for 90 seconds with various microdoses of alteplase (Fig. 2A, C). The chip was subsequently perfused with porcine plasma for 25 min (matched for physiological shear stress of 30 dyn/cm²). Conventional intravenous (IV) drug infusion (10 mg dose) resulting in a low systemic alteplase concentration, was mimicked by perfusing microthrombi with porcine plasma containing 2 µg/ml alteplase (Fig. 2B, C). Results Thrombolysis after CFI was concentration dependent, with the lowest microdose (0.3 mg) achieving 24% lysis of the thrombus area and the highest microdose (1.5 mg) achieving 60% lysis. In contrast, conventional IV drug infusion (corresponding to 10 mg alteplase IV dose) only achieved 10% lysis and was not significantly higher than the control perfused with pure porcine plasma. Conclusion Our findings suggest that intracoronary CFI is more efficient at achieving porcine microthrombus lysis than the current standard of IV bolus infusion (2 µg/ml alteplase in the circulating blood). Intracoronary CFI microdosing of fibrinolytic drugs using a drug-delivering catheter is a promising therapeutic approach for treating embolising MVO with a reduced systemic drug burden. Importantly, our intracoronary CFI approach achieves locally 6–40 times higher drug concentrations than a conventional IV drug infusion while reducing the total drug dose 60–300 times (Fig. 2C).