A single-stage pull-through (SSPT) is the most commonly performed procedure for Hirschsprung disease (HSCR) and has been shown to be better than multi-stage procedures. However, performing a SSPT in the neonatal period or early in infancy is a risk factor for an inaccurate diagnosis, post-operative enterocolitis, and a protracted post-operative recovery. The present study was primarily designed to evaluate the feasibility and efficacy of home rectal irrigation in the neonatal period and early in infancy, followed by a delayed and planned SSPT in a prospective cohort with HSCR. Between January 2014 and December 2016, a total of 147 neonates diagnosed with HSCR were enrolled in the study. Six patients were excluded as a result of ganglion cells found in second rectal biopsies after the neonatal period. One hundred twenty-two patients successfully underwent 2-4months of home rectal irrigation during the neonatal period, followed by a SSPT procedure after the neonatal period (group A, n = 122). Nineteen patients were not candidates for home rectal irrigation, and thus, colostomies were performed during the neonatal period followed by multi-stage procedures after the neonatal period (group B, n = 19). One hundred twenty-two healthy children, age- and gender-matched to group A were enrolled as the healthy control group for assessment of nutrition status (group C, n = 122). The birth weight, gender ratio, aganglionic segment, age, and Hirschsprung-associated enterocolitis (HAEC) score at the time of HSCR diagnosis were measured to evaluate the feasibility of home rectal irrigation in neonates and early in infancy. The nutritional indices, including weight, body length, serum albumin, serum prealbumin, serum retinol-binding protein, and incidence of HAEC after 2-4 successful home rectal irrigation, were used to assess the efficacy of home rectal irrigation. Anastomotic strictures or leakage, perianal excoriation, frequency of defecation, and morbidity of post-operative HAEC were recorded to evaluate the beneficial effects to pull through (PT), which were facilitated by home rectal irrigation. Higher HAEC scores and older age at the time of diagnosis of HSCR were associated with group B, compared to group A (4.34 ± 1.25 vs. 11.0 ± 2.56 [t = 18.20, p < 0.05] and 2.8 ± 1.46days vs. 12.1 ± 5.3days [t = 16.10, p < 0.05], respectively). The ratio of rectosigmoid HSCR to non-rectosigmoid HSCR was higher in group A than group B (104/18 vs. 4/15 [χ2 = 34.29, p < 0.05]). There were no differences in birth weight, weight at the time of diagnosis of HSCR, and gender ratio between groups A and B. There were no differences in birth weight, birth length, post-home rectal irrigation age, post-home rectal irrigation weight, post-home rectal irrigation length, and post-home rectal irrigation serum albumin between groups A and C (3.47 ± 0.42kg vs. 3.48 ± 0.40kg [t = 0.10, p > 0.05], 50.02 ± 0.49cm vs. 50.05 ± 0.46cm [t = 0.61, p > 0.05], 98.59 ± 13.34days vs. 97.83 ± 13.58days [t = 0.44, p > 0.05], 6.77 ± 0.66kg vs. 6.97 ± 0.87kg [t = 1.95, p > 0.05], 61.55 ± 2.14cm vs. 61.70 ± 2.07cm [t = 0.59, p > 0.05], and 41.78 ± 2.42g/L vs. 41.85 ± 2.37g/L [t = 0.22, p > 0.05], respectively). The rate of HAEC in the period of home rectal irrigation in group A was low; however, the post-home rectal irrigation serum prealbumin level and retinol-binding protein were significantly lower in group A than group C (0.15 ± 0.04g/L vs. 0.17 ± 0.05g/L [t = 3.50, p < 0.05] and 22.51 ± 7.53g/L vs. 30.57 ± 9.26g/L [t = 7.46, p < 0.05], respectively). There were no anastomotic strictures or leakage after definitive PT performed in group A. The frequency of defecation ranged from 2-6 times per day, 10 patients had perianal excoriation 3months after PT, and 11 patients had post-operative HAEC during 6months of follow-up after PT. Home rectal irrigation in neonates and early in infancy, followed by a delayed and planned SSPT is feasible and effective in patients with HSCR, and could be beneficial to definitive PT. However, for patients with an extended aganglionic segment, older age, or high HAEC score at the time of diagnosis of HSCR, rectal irrigation maybe not suitable. This was a prospective comparative study designed to evaluate the effects of home rectal irrigation for facilitating and enhancing recovery after PT, and was registered at Clinical Trials.gov as NCT02776176.