Experiments were conducted to optimize transport conditions of nursery-reared juvenile milkfish in a closed-bag transport system. Combined effects of temperature (25°C–27°C, 20°C–22°C, and 15°C–17°C) and anesthetics (2-phenoxyethanol at 80 mgL−1 for transport sedation) on the survival of juvenile milkfish, Chanos chanos, were evaluated. Another experiment evaluated transport densities of 200, 400, 600, 800, and 1,000 gL-1 for 4-, 8-, 12-, 16-, and 20-h duration. The study showed that a temperature of 20°C–22°C in combination with anesthetic (2-phenoxyethanol) application was the optimum condition for long-duration confinement of milkfish juveniles in transport bags. Milkfish density of 600 gL−1 was found to be optimum for 12 h, 400 gL−1 for 16 h, and 200 gL−1 for 20 h of transport duration. These results provide a practical protocol for the high-density transport of juvenile milkfish from nursery to the growout production facilities.