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Background Long-term survivors after hematopoietic stem cell transplant (HSCT) may encounter issues that lower their quality of life. Data on the psychological effects of HSCT in childhood are scarce. Morever, the effect of HSCT on cognitive function is regarded as a key issue. Objectives Assess survivors of HSCT for cognitive or psychological affection and explore their quality of life after HSCT. Patients and methods A cross-sectional Study was conducted on 25 long-term survivors of HSCT. The children psychological aspects were assessed using Pediatric Symptom Checklist (PSC), Self-esteem score of Rosenberg, Children Depression Inventory, Children anxiety scale, Pediatric Quality of Life (QOL),Wechsler III for IQ. Results The psychological evaluation scores of 14 males and 11 females showed that 28% of survivors had mild anxiety, 40% had a moderate anxiety and 32% had sever anxiety, according to PSC, 36% only reported emotional and behavioral problems. Regarding depression scale, 36% had mild depression and 12% had moderate depression and only 8% had severe depression. There was significant positive correlation between the survival period after transplantation and IQ (P value 0.008). There was statistically significant association between post-transplant infections and lower QOL (P value 0.047). Another significant association between chronic GVHD and lower self-esteem score (P value 0.031). Conclusion These findings brought to light ongoing issues with the cognitive and psychological evaluation of pediatric long-term survivors of HSCT, as well as the impact of chronic GVHD and post-transplant infection on their psychological evaluation, particularly on self-esteem score and QOL, respectively. Therefore, it is crucial to create focused treatments for pediatric HSCT care in Egypt. Psychologists must be a part of the transplantation care team. [ABSTRACT FROM AUTHOR]