Abstract Background The EASL cystic liver disease guideline states that drug penetration at the site of infection (liver cyst) is essential for successful treatment, but pharmacokinetic (PK) data on cyst penetration are limited. Objectives This study aims to investigate tissue penetration of four antibiotics in non-infected liver cysts and explores influencing factors. Methods We performed a prospective, randomized single-dose PK-study. Before percutaneous drainage of a non-infected liver cyst, an intravenous (IV) dose of either ciprofloxacin and piperacillin/tazobactam (group 1); or co-trimoxazole (trimethoprim/sulfamethoxazole) and doxycycline (group 2) was given. Cyst fluid was collected during drainage. Blood samples were obtained before, during and after drainage (within 12 h). Drug concentrations were measured with a validated LC-MS/MS. Primary outcome was liver cyst penetration, defined as the cyst-fluid-to-plasma concentration ratio (%) expressed as median (IQR). Results We included 20 patients, and 21 liver cysts were drained (group 1: n = 11, group 2: n = 10). Median drained cyst volume was 700 mL. Median time between infusion and drainage was 139 min (IQR 120–188 min). Median cyst-fluid-to-plasma concentration ratio was 4.2% (IQR 1.6%–8.9%) for ciprofloxacin, 0.3% (IQR 0.0%–1.3%) for piperacillin, 0.2% (IQR 0.0%–1.3%) for tazobactam, 12.2% (IQR 6.3%–16.1%) for trimethoprim, 0.4% (IQR 0.2%–3.8%) for sulfamethoxazole and 1.6% (IQR 0.9%–2.3%) for doxycycline. Time between trimethoprim infusion and cyst drainage was correlated with increased cyst-fluid-to-plasma concentration ratio (P < 0.01). Conclusions Trimethoprim and ciprofloxacin have the highest penetration ratios amongst antibiotics tested. We found that liver cyst penetration varies widely between drugs after a single IV dose. Clinical trial number NTR8499 The trial was originally registered in the Netherlands Trial Register (ID: NL7290), which was converted to the International Clinical Trials Registry Platform in 2022.