With the objective to develop an indoor tank seed rearing system for pearlspot (Etroplus suratensis), effects of three stocking densities in presence or absence of soil base were evaluated on growth, weight variation, survival and body composition in a 60‐day trial. The experiment had a 3 × 2 factorial design with three levels of stocking density (150, 300 and 450 fish m−3) and two levels of soil base (with and without) in triplicates. Pearlspot fry (27.5 ± 0.5 mm/0.39 ± 0.02 g) were stocked in experimental tanks (Length×Breadth×Height: 0.65 × 0.50 × 0.48 m) and fed with a formulated diet containing 29.85% crude protein. Increasing the stocking density from 150 to 450 fish m−3 significantly decreased the growth (average body weight and total length), daily weight gain, specific growth rate and survival (P < 0.001) and increased the feed conversion ratio (P < 0.01). Significantly lower growth and survival were observed in treatment having soil base compared with that of without soil base (P < 0.001). However, coefficients of variation at harvest weight and body composition of fingerlings were independent to stocking density and presence or absence of soil base (P > 0.05). A significant positive interaction effect of stocking density and presence or absence of soil base was observed on average body weight (P < 0.05) and survival (P < 0.001) of pearlspot fingerlings. This study suggests that stocking density of 150 fish m−3 without soil base in tanks would be appropriate for raising pearlspot fingerlings in brackishwater indoor seed rearing system.