BackgroundThe increasing spread of fluoroquinolone resistant enteric bacteria is a global public health concern. Children recently discharged from the hospital are at high risk of carriage of antimicrobial resistance (AMR) due to frequent exposure to antimicrobials during inpatient stays. This study aimed to determine the prevalence, correlates of ciprofloxacin (CIP) non-susceptibility, and distribution of plasmid-mediated quinolone resistance (PMQR) genes inEscherichia coli (E. coli)andKlebsiellaspp isolated from children under five years being discharged from two Kenyan Hospitals.MethodsE. coliandKlebsiellaspp were isolated from fecal samples from children discharged from hospital and subjected to antimicrobial susceptibility testing (AST) by disc diffusion and E-test. CIP non-susceptible isolates were screened for seven PMQR genes using multiplex polymerase chain reaction (PCR). Poisson regression was used to determine the association between the carriage of CIP non-susceptible isolates and patient characteristics.ResultsOf the 280 CIP non-susceptible isolates: 188E. coliand 92Klebsiellaspp isolates identified among 266 discharged children, 195 (68%) were CIP-non-susceptible with minimum inhibitory concentrations (MICs) of ≥ 1 µg/mL. Among these 195 isolates, 130 (67%) had high-level CIP MIC =  ≥ 32 µg/mL). Over 80% of the isolates had at least one PMQR gene identified:aac(6’)lb-cr (60%), qnrB (24%),oqxAB (22%), qnrS (16%),andqepA (6%),however,qnrAwas not identified in any isolates tested. Co-carriage ofqnrBwithacc(6’)-lb-crwas the most predominant accounting for 20% of all the isolates. Ceftriaxone use during hospital admission and the presence of extended spectrum beta-lactamase (ESBL) production were significantly associated with the carriage of CIP non-susceptibleE. coliandKlebsiellaspp.ConclusionCIP non-susceptibility is common amongE. coliandKlebsiellaspp isolated from hospital discharged children in Kenya. Carriage and co-carriage of PMQR, including the newly identifiedqepAgene, were frequently observed. These findings suggest that children leaving the hospital may serve as an important reservoir for transmission of resistantE. coliandKlebsiellaspp to the community. Enhanced surveillance for AMR determinants is critical to inform interventions to control antimicrobial-resistant bacteria.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-023-02849-2.