Introduction The randomized PRAGUE-17 trial demonstrated noninferiority of left atrial appendage closure (LAAC) to non-vitamin K anticoagulants (NOACs) for the prevention of major cardiovascular or cerebrovascular events. However, the left atrial appendage is an important source of natriuretic peptides and plays a role in left atrial reservoir function. Changes of heart failure (HF) biomarkers after LAAC compared to NOAC has not been studied. The aim of the study was to compare the changes in concentrations of HF biomarkers between LAAC and NOAC patients. Methods Of 402 patients randomized in the PRAGUE-17 trial, biomarkers were analyzed in 144 patients (73 in the NOAC and 71 in the LAAC group). Both groups had similar baseline characteristics. Serum concentration of NT-proBNP, NT-proANP, Galectin-3, and GDF-15 were measured at baseline (before the procedure in the LAAC group), at the 6-month (and at 24-month for NT-proBNP) follow-up timepoint. Results There were no significant differences in baseline, 6 month, and delta (delta = baseline - 6 month) concentrations of NT-proANP between the groups (NOAC: baseline 2.6 [0.5; 4.9], 6-month 3.1 [1.8; 4.8], p = .068; LAAC: baseline 3.3 [1.1; 4.6], 6-month 2.6 [0.9; 5.3], p = .51; p value for delta in concentrations between groups = 0.42). Similarly, there were no significant differences in baseline, 6, 24 months, and delta concentrations of NT-proBNP between the groups (NOAC: baseline 461.0 [113.5; 1342.0], 6 month 440.0 [120.5; 1291.5], 24 month 798 [274; 2236], p = .39; LAAC: baseline 421.0 [100.0; 1320.0], 6 month 601.0 [145.0; 1230.0], 24 month 855 [410; 1367], p = .28; p value for delta in concentrations between groups = 0.73 at 6 months, and 0.58 at 24 months). Finally, no significant differences were present in baseline, 6 month, and delta concentrations of Galectin-3 and GDF-15 between the two groups. Conclusion LAAC did not significantly influence the levels of HF biomarkers 6 months after the procedure.