Background The treatment for children and adolescents with acute lymphoblastic leukemia (ALL) can lead to multiple adverse effects, including poor physical capacity and muscle weakness. This study aimed to determine which is more effective, aerobic exercises or modified strength training program, on muscle strength and quality of life (QOL) for children with ALL. Results In terms of muscle strength, there was a significant difference (P < 0.05) in selected group of muscles elbow flexors, shoulder abductors, hip flexors, knee extensors, and ankle dorsiflexors at both sides in group B compared with group A, whereas there was no significant difference (P > 0.05) between groups on QOL. Conclusion The outcomes of the study showed that there was a significant difference in the selected group of muscles at both sides in group B compared with group A; thus, the modified strength training program is more effective for muscle strength of children with ALL than aerobic training, but there was no significant difference between them on QOL. Trial registration The clinical trial registered in clinicaltrials.gov with an identifier number NCT03147365