Abstract Background Pulsed field ablation (PFA) represents a novel promising non-thermal alternative in non-pharmacological treatment of atrial fibrillation (AF). However, infrequent cases of acute renal failure secondary to intravascular haemolysis after a PFA procedure have been described. Objective To investigate the impact of ablation technology (PFA vs. radiofrequency ablation (RFA)) on the level of plasma cell-free haemoglobin (CFH) and the concentration of serum neutrophil gelatinase-associated lipocalin (NGAL) as a marker of tubular injury. Methods This was a prospective observational trial. In a consecutive cohort of patients who underwent AF ablation (PFA of RFA), blood samples were drawn just before the procedure (Sample 1: CFH and NGAL), immediately after the procedure (Sample 2: CFH) and one day after the procedure (Sample 3: CFH and NGAL). Plasma CHF level and serum NGAL concentration were analysed using the ELISA technique. Results Among 70 patients enrolled (mean age 64.3 ± 10.3 years, 61 % male), 23 underwent RFA and 47 PFA (22 pulmonary vein isolation (PVI) only and 25 PVI with other additive lesions). Baseline serum creatinine levels of both groups were comparable (91.7 ± 22.1 µmol/L vs. 88.8 ± 22.1 µmol/L P = 0.44). In the PFA cohort, a significant peak of CFH concentration was observed just after the procedure with a subsequent decrease within 12 hours (Sample 1 vs. Sample 2: 93.4 ± 65.1 µg/mL vs. 2394.9 ± 1966.1 µg/mL P < 0.001, Sample 1 vs. Sample 3: 93.4 ± 65.1 µg/mL vs. 97.2 ± 68.5 µg/mL P = 0.75). No significant differences were observed in the RFA cohort. Compared to baseline, neither the PFA nor the RFA group showed a significant difference in NGAL levels (PFA 98.6 ± 31.7 ng/mL vs. 98.5 ± 38.1 ng/mL P = 0.78, RFA 108.3 ± 33.8 ng/mL vs. 116.3 ± 32.2 ng/mL P = 0.49). Conclusions Compared to RFA, PFA leads to significant peri-procedural haemolysis. However, no differences in the concentration of the tubular injury marker NGAL were observed on the first day after the procedure.