A 20-day 3 ∗ 3 factorial experiment was conducted in 100 L HDPE experimental tanks to investigate the effect of the C/N ratio (10, 15, and 20) and stocking density (3, 4, and 5 spawn L−1) on Gibelion catla spawn nursery rearing in the indoor biofloc system. Rice bran was used as the carbon source for manipulating C/N ratios. Each treatment was stocked with catla spawn of average length (6.7 ± 0.4 mm) and average weight (1.6 ± 0.2 mg). Water parameters showed that increasing the C/N ratio from 10 to 20 significantly (
p
<
0.05
) reduced total ammonia nitrogen (TAN) and nitrite nitrogen (NO2-N) and increased nitrate nitrogen (NO3-N) in the water. The insignificant difference (
p
>
0.05
) and lowest final average length, average length gain, average weight gain, and specific growth rate (SGR) were recorded in C/N ratios of 10 and 15 compared to a C/N ratio of 20. A significant difference (
p
<
0.05
) in survival was observed with the increasing C/N ratio. Increasing the fish stocking density resulted in higher mortality. However, a higher amount of fry produced was observed in the treatments with 3 and 4 spawn L−1. Crude protein content increased significantly (
p
<
0.05
) with the increasing C/N ratio with higher content in C/N 20. No significant difference (
p
>
0.05
) in proximate composition of biofloc was observed in different stocking density groups. In conclusion, the application of the biofloc technology with a C/N ratio of 20 at a stocking density of 4 spawn L−1 could be recommended to increase the production of catla fry in the indoor biofloc system.