The aim was to compare the renal dynamic scan (RDS) performed with technetium-99-L,L-ethylene dicysteine (99mTc-L,L-EC) and technetium-99-mercaptoacetyltriglycine (99mTc-MAG3) in children with pelviureteric junction (PUJ) obstruction. A retrospective study was carried out and children with PUJ obstruction who had RDS performed with both 99mTc-L,L-EC and 99mTc-MAG3. Children with any intervention in between the two scans or a gap of more than 2 months in between renal scans were excluded. The dose of each radiotracer used was 0.1 mCi/kg (3.7 MBq/kg), with a minimum dose of 1 mCi (37 MBq). RDS was performed using the F+0 protocol. The differential renal function, Tmax, T1/2, drainage pattern, and hepatic uptake of the radiotracer were recorded and compared. A Bland–Altman plot was used to assess agreement between the two radiotracers. Sixteen children were included in the study. A total of 18 obstructed and 14 normal renal units were available to us for study. The values of differential renal function as well as Tmax and T1/2 of the two radiotracers were in agreement. In three obstructed kidneys in which T1/2 on 99mTc-MAG3 was greater than 20 min, 99mTc-L,L-EC showed T1/2 values of 13.3 min or less. 99mTc-L,L-EC showed nonobstructive drainage in three patients who had shown partial obstruction on 99mTc-MAG3 scan. The hepatic uptake of 99mTc-L,L-EC was also lower compared with 99mTc-MAG3. To conclude 99mTc-L,L-EC is a useful radiotracer for the evaluation of children with PUJ obstruction, with better assessment of drainage and lower hepatic uptake compared with 99mTc-MAG3.