Fucoxanthin (FUCO) is a light- and heat-sensitive marine xanthophyll carotenoid, present in brown algae that render physiological properties as anti-oxidants. In this study, nanoencapsulation is an approach adopted to improve bioavailability of FUCO by using ionic-gelation method with polymeric chitosan (CS) dispersed in glycolipid (GL), as a carrier. Further, the aim was to investigate adverse effect of acute and sub-acute toxicity of chitosan nanogels (CS-NGs) loaded with FUCO+GL in rats. In the acute toxicity study, FUCO was fed to rats at doses of 0.1, 1, 10 and 100 mg/kg body weight (BW). In the sub-acute toxicity study, FUCO was fed at doses of 1 and 10 mg/kg BW for 28 days. In both the studies, no mortality and abnormalities in gross morphology were observed. Acute toxicity study revealed that the LD50 of FUCO in CS-NGs is higher than 100 mg/kg BW. No postprandial plasma levels of FUCO were detected. However, fucoxanthinol (FUOH), a hydrolytic metabolite of FUCO was detected in a dose dependent manner (P < 0.01). Compared to the control group(s), no dose-related toxic effects of CS-NGs with FUCO + GL were found in haematological, histopathological, plasma biochemical indices, etc. The no-observed-adverse-effect level (NOAEL) for CS-NGs with FUCO + GL in rats was 10 mg/kg/day. To conclude, no apparent adverse effect of CS-NGs with FUCO + GL demonstrating CS could be a promising polymer matrix for safe delivery of FUCO. This is the first study to demonstrate the safety assessment of CS-NGs with FUCO + GL.