Background This study aimed to evaluate the usefulness, from a therapeutic perspective, of classifying the subtypes of functional childhood constipation using a colon transit time (CTT) test. Methods A total of 190 children were enrolled in this study, which was based on data collected from a defecation diary, a CTT test, and medical records. Results Polyethylene glycol (PEG) 4000 was prescribed in 51.1% (N= 47/92) of normal transit type constipation cases (NT) and 91.8% (N= 90/98) of abnormal transit type constipation cases (P< 0.001). In terms of the subtype of CTT test, PEG 4000 was prescribed in 51.1% (N= 47/92) of NT cases, 96.2% (N= 25/26) of outlet obstruction type cases (OT), and 90.3% (N= 65/72) of slow transit type cases (ST) (P< 0.001). Polyethylene glycol 4000 was administered in 97.2% (N= 35/36) of the fecal incontinence group and 66.2% (N= 102/154) of the non-fecal incontinence group (P< 0.001). In the non-fecal incontinence group, PEG 4000 was prescribed in 47.3% (N= 40/84) of NT cases, 94.4% (N= 17/18) of OT cases, and 86.5% (N= 45/52) of ST cases (P< 0.001). In the fecal incontinence group, PEG 4000 was prescribed in 87.5% (N= 7/8) of NT cases, 100% (N= 8/8) of OT cases, and 100% (N= 20/20) of ST cases (P= 0.165). Conclusions Subtype classification of functional constipation based on the CTT test provides important information for the initial choice of drugs in children.