This study aims to formulate and characterize the emulsion of Morinda citrifolia L. (Noni fruit) extract in virgin coconut oil (VCO) using the Phase Inversion Composition method (PIC). The chemical compositions with bioactivities in noni fruit extracts obtained from Soxhlet extraction method were analyzed by using Gas Chromatography-Mass Spectrometry to understand their potential uses. To formulate VCO-based emulsion, different types of surfactants (Cremophor EL, Cremophor RH 40, and Tween 80) and co-surfactants (Propylene glycol, Ethylene glycol, and Ethanol) were varied in concentration. The characteristics of VCO-based emulsions in terms of droplet size and stability were analyzed to find the optimal condition for stable emulsion. Among three types of surfactants, Cremophor RH 40 mixed with propylene glycol or ethylene glycol provided the most stable VCO-based emulsion in nanoscale droplet size with the minimal droplet size at 332 nm. The noni extracts were mixed in the optimized VCO-based formula at the VCO's concentration of 6, 8, and 10%. The results showed that the addition of noni extracts increased the droplet size of emulsion from nanometer scale to micrometer scale and reduced the emulsion stability. At the optimal condition, the mixture containing 4.5% VCO, 1.5% propylene glycol, and 0.3% Noni extract showed the smallest droplet size (1.1–1.85 μm), which was in the range of most commercial emulsions, with good stability in a 5-day period. This study provides a promising approach to formulate stable emulsions with low levels of surfactant and co-surfactant, which is extensively significant for commercial delivery systems.