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Background Assessment of pain in children is an important aspect of pain management and can be performed by observational methods or by self-assessment. The Faces Pain Scale-Revised (FPS-R) is a self-report tool which has strong positive correlations with other well established self-report pain intensity measures. It has been recommended for measuring pain intensity in school-aged children (4 years and older). The objective of this study is to compare the concordance and the preference for two versions, electronic and paper, of the FPS-R, and to determine whether an electronic version of the FPS-R can be used by children aged 4 and older. Methods The study is an observational, multicenter, randomized, cross-over, controlled, open trial. Medical and surgical patients in two pediatric hospitals (N = 202, age 4-12 years, mean age 8.3 years, 58% male) provided self-reports of their present pain using the FPS-R on a personal digital assistant (PDA) and on a paper version. Paper and electronic versions of the FPS-R were administered by a nurse in a randomized order: half the patients were given the PDA version first and the other half the paper version first. The time between the administrations was planned to be less than 30 minutes but not simultaneous. Two hundred and thirty-seven patients were enrolled; 35 were excluded from analysis because of misunderstanding of instructions or abnormal time between the two assessments. Results Final population for analysis comprised 202 children. The overall weighted Kappa was 0.846 (95%CI: 0.795; 0.896) and the Spearman correlation between scores on the two versions was rs = 0.911 (p < 0.0001). The mean difference of pain scores was less than 0.1 out of 10, which was neither statistically nor clinically significant; 83.2% of children chose the same face on both versions of the FPS-R. Preference was not modified by order, sex, age, hospitalization unit (medical or surgical units), or previous analgesics. The PDA was preferred by 87.4% of the children who expressed a preference. Conclusion The electronic version of the FPS-R can be recommended for use with children aged 4 to 12, either in clinical trials or in hospitals to monitor pain intensity.