Objectives This study aims to determine the prevalence of maltreatment experienced by institutionalized children prior to their admission to Charitable Children's Institutions (orphanages) in western Kenya, and to describe their socio-demographic characteristics, reasons for admission, and the factors associated with prior experiences of maltreatment. Methods A systematic file review was undertaken in five CCIs. Demographic, prior caregiving settings and maltreatment data were extracted. Forms of maltreatment were recorded according to WHO and ISPCAN guidelines. Logistic regression was used in bivariate and multivariable analyses of factors associated with reasons for placement and forms of maltreatment. Results A total of 462 files were reviewed. The median (interquartile range) age of children was 6.8 (5.08) years at admission, 56% were male, and 71% had lost one or both parents. The reasons for admission were destitution (36%), abandonment (22%), neglect (21%), physical/sexual abuse (8%), and lack of caregiver (8%). The majority of child and youth residents had experienced at least one form of maltreatment (66%): physical abuse (8%), sexual abuse (2%), psychological abuse (28%), neglect (26%), medical neglect (18%), school deprivation (38%), abandonment (30%), and child labor (23%). The most common reason for non-orphans to be admitted was maltreatment (90%), whereas the most common reason for orphans to be admitted was destitution (49%). Girls (adjusted odds ratio, AOR: .61, 95% CI: .39–.95) and orphans (AOR: .04, 95% CI: .01–.17) were both independently less likely to have a history of maltreatment irrespective of whether it was the reason for admission. Children whose primary caregiver had not been a parent (AOR: .36, 95% CI: .15–.86) and orphans (AOR: .17, 95% CI: .06–.44) were less likely to have been admitted for maltreatment, while children who were separated from siblings were more likely to have been admitted for maltreatment (AOR: 1.62, 95% CI: 1.01–2.60). Conclusions The high prevalence of maltreatment prior to admission, particularly among nonorphans, suggests the need for better child abuse and neglect prevention programs in communities, and psychosocial support services in institutions. The significant proportion of children admitted for poverty, predominantly among orphans, indicates that community-based poverty-reduction programs might reduce the need for institutionalization.