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Diarrhoea is a major contributor to childhood morbidity and mortality in developing countries, with diarrhoeagenic <i>Escherichia coli</i> being among the top aetiological agents. We sought to investigate the burden and describe the diarrhoeagenic <i>E. coli</i> pathotypes causing diarrhoea among children in peri-urban areas of Lusaka, Zambia. This was a facility-based surveillance study conducted over an 8-month period from 2020 to 2021. Stool samples were collected from children aged 0–3 years presenting with diarrhoea at five peri-urban health facilities in Lusaka. Stool samples were tested for diarrhoeagenic <i>E. coli</i> using the Novodiag bacterial GE+^® panel, a platform utilising real-time PCR and microarray technology to detect bacterial pathogens. Of the 590 samples tested, diarrhoeagenic <i>E. coli</i> were detected in 471 (76.1%). The top three pathogens were enteropathogenic <i>E. coli</i> 45.4% (<i>n</i> = 268), enteroaggregative <i>E. coli</i> 39.5% (<i>n</i> = 233), and enterotoxigenic <i>E. coli</i> 29.7% (<i>n</i> = 176). Our results revealed that 50.1% of the diarrhoeagenic <i>E. coli</i> positive samples comprised multiple pathotypes of varying virulence gene combinations. Our study demonstrates a high prevalence of diarrhoeagenic <i>E. coli</i> in childhood diarrhoea and the early exposure (<12 months) of children to enteric pathogens. This calls for the early implementation of preventive interventions for paediatric diarrhoea.