Abstract Background Dysregulation of autophagy is known to have detrimental effects on cardiac function. Yet, the autophagy-lysosome pathway in the context of ischemia is still widely unexplored. Fyco1 is highly expressed in the heart and facilitates transport of autophagosomes in cardiomyocytes, thereby enhancing global autophagic flux. Purpose The purpose of our study was to study the potentially beneficial effects of activation of autophagy via FYCO1 on cardiac remodeling post myocardial infarction. Methods FYCO1-Tg mice were crossbred with RFP-EGFP-LC3-Tg reporter mice (FYCO1-TGxRGFP) to enable analysis of autophagic flux in vivo using confocal microscopy. Myocardial ischemia was induced by permanent ligation of left anterior descending artery (LAD). Mice were analyzed 3 and 30 days post LAD ligation. Cardiac function (ejection fraction, EF) was measured by echocardiography. Fibrosis and Infarct size (%) were assessed in Masson’s Trichrome staining. Autophagy activity was analysed by Western blot for p62 and LC3 II. Furthermore, Evans blue/TTC staining was performed to assess the area at risk and to define perfused, ischemic and necrotic area post LAD ligation. Results Under conditions of FYCO1 overexpression isolated cardiomyocytes were capable to remain a status of activated autophagy in hypoxia; presented with significantly increased protein levels of p62 (ctrl: 1±0,02; OE: 3,1±0,4) and LC3 II (ctrl: 1±0,05; OE: 5,5±0,4). In FYCO1-TGxRGFP mice we observed an overall increased autophagic flux demonstrated by significantly increased p62 expression (WT LAD: 2,9±0,4; TG LAD:4,0±0,5) and LC3 II protein levels (WT LAD: 1,6±0,2; TG LAD:14,0±1,4) post LAD ligation. While WT mice revealed accumulation of autolysosomes 30 days post LAD ligation as assessed by confocal microscopy (WT autophagosomes: 1±0,4; WT autolysosomes: 38,6±3,8), in FYCO1-TGxRGFP mice the ratio between autophagosomes and autolysosomes remained even (TG autophagosomes:43,3±5,1; TG autolysosomes: 73,5±12,4), suggesting preservation of adequate autophagic flux. In Evans blue/TTC staining, FYCO1-TGxRGFP mice demonstrated comparable ischemic but a markedly decreased necrotic area (ischemic: 1,9±1,8%; necrotic: 37,1±11,5%) of the LV as compared to WT (ischemic: 2,1±1,9%; necrotic: 53,4±31,4%). Fibrosis (WT: 19,6±1,8%; TG: 10,6±1,6%) and infarct size (WT: 34,5 ±3,9%; TG: 5,5±2%) was found significantly decreased in FYCO1-TGxRGFP-mice. Importantly, global heart function of FYCO1-TGxRGFP-mice was significantly improved post LAD compared to WT (EF WT: 36,7±6,3%; TG: 46,3±18,3%). Conclusion Our study demonstrates that activation of autophagy via FYCO1 protects against accumulation of autolysosomes and therefore protects against adverse cardiac remodeling and improves cardiac function post myocardial ischemia. These findings may offer translational potential in enhancing autophagic flux in the context of myocardial ischemia.