The health benefits of long-chain omega-3 polyunsaturated fatty acid (LCn-3PUFA) intake have been well documented. However, currently, the consumption of oily fish (the richest dietary source of LCn-3PUFA) in the UK is far below the recommended level, and the low digestibility of LCn-3PUFA bulk oil-based supplements from triglyceride-based sources significantly impacts their bioavailability. LCn-3PUFA-rich microalgal oil offers a potential alternative for populations who do not consume oily fish, and nanoemulsions have the potential to increase LCn-3PUFA digestibility and bioavailability. The aims of this study were to produce stable algal oil-in-water nanoemulsions with ultrasonic technology to increase DHA digestibility, measured using an in vitro digestion model. A nanoemulsion of LCn-3PUFA algal oil was developed with 6% w/w emulsifiers: lecithin (LE) or an equal ratio of Tween 40 (3%) and lecithin (LTN) (3%), 50% w/w, algal oil and 44% w/w water using rotor-stator and ultrasound homogenization. The in vitro digestion experiments were conducted with a gastric and duodenal digestion model. The results showed the creation of nanoemulsions of LCn-3PUFA algal oils offers potentially significant increases in the bioavailability of DHA in the human body. The increase in digestibility can be attributed to the smaller particle size of the nanoemulsions, which allows for higher absorption in the digestive system. This showed that the creation of nanoemulsions of LCn-3PUFA algal oils offers a potentially significant increase in the bioavailability of DHA in the human body. The LE and LTN nanoemulsions had average droplet sizes of 0.340 ± 0.00 µm and 0.267 ± 0.00 µm, respectively, but the algal oil mix (sample created with same the components as the LTN nanoemulsion, hand mixed, not processed by rotor-stator and ultrasound homogenization) had an average droplet size of 73.6 ± 6.98 µm. The LTN algal oil nanoemulsion was stable in the gastric and duodenal phases without detectable destabilization; however, the LE nanoemulsion showed signs of oil phase separation in the gastric phase. Under the same conditions, the amount of DHA digested from the LTN nanoemulsion was 47.34 ± 3.14 mg/g, compared to 16.53 ± 0.45 mg/g from the algal oil mix, showing DHA digestibility from the LTN nanoemulsion was 2.86 times higher. The findings of this study contribute to the insight of in vitro DHA digestion under different conditions. The stability of the LTN nanoemulsion throughout digestion suggests it could be a promising delivery system for LCn-3PUFAs, such as DHA, in various food and pharmaceutical applications.