Expanding the culture of juvenile sandfish Holothuria scabra faces limitations due to constrained space and the associated high operational costs. To reduce the hatchery rearing phase, floating fine mesh nets (1 mm) hapas (2 m × 1 m × 1.2 m) have been established as a viable ocean nursery system for the mass production of >3 g juvenile H. scabra in the eutrophic coastal waters of Bolinao, Pangasinan, Philippines. Subsequently, ocean nursery pens are utilized as an intermediate nursery to grow juvenile sandfish larger sizes (>20 g) prior to release for grow out in the sea ranch or for restocking managed areas. This study explored the possibility of shortening the floating hapa rearing period and use of sea pens in rearing smaller juvenile sandfish (≤1 g; 2.4 ± 0.3 cm). Comparisons on the growth and survival of juvenile sandfish were determined in a 90-day field experiment using two types of pens (2 m2): covered (n=9) and uncovered (n=9), with the same batch of juveniles maintained in the floating hapa (n=10) as control. Average weights were significantly higher in pens with (27.9 ± 11.1 g) or without cover (27.2 ± 14.8 g) than in the floating hapa (8.2 ± 2.4 g). The burying behavior of juvenile sandfish also did not differ significantly between the type of pens, with most individuals able to bury within a 24-h period. However, juvenile survival was significantly higher (82.9 ± 13.4%) in the floating hapa than both pens, with covered (9.2 ± 19.9%) having significantly lower survival than uncovered (29.7 ± 21.4%) pens. Earlier release of juveniles from the floating hapa to the sea pens produced larger juvenile over a shorter period but fewer numbers. Although pen rearing reduces the vulnerability of juveniles to varying sea surface conditions, juveniles were exposed to benthic predators such as crabs thus, the low survival even in the covered pens. Further studies to improve the survival of small juveniles in the ocean nursery pens may reduce the period to grow the juveniles to release sizes > 20 g; likewise, the costs of ocean nursery rearing compared to floating hapas. This will also allow more batches of juveniles to be reared during the 5–6-month dry season without increasing investments in additional floating hapas and pens. The two phases of ocean nursery systems can be further optimized to increase juvenile production for grow-out and restocking.