Lignin is the second most abundantly occurring biopolymer in the biosphere, and is present in plant cell walls, along with cellulose and hemicellulose. The use of lignin, across sectors, has increased in the past few years, due to its availability, cost-effectiveness, biodegradability, and eco-friendliness. In this investigation, we isolated lignin samples from Borassus flabellifer biomass, and assessed its thermal and antioxidant properties. Furthermore, its cytotoxic properties were analyzed using cell viability and acridine orange/ethidium bromide staining assays, in human mesenchymal stem cells (hMSCs), as an in vitro model. The results of thermal stability tests indicated that more than 40% of the weight was retained in L1, L2, L4, L5, L6, L7 and L9, after treatment at 600 °C, due to lignin's high thermal stability. The radical scavenging potential of the lignin samples was studied by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. L2 had the highest antioxidant activity. The results of the cell viability assays indicated that lignin reduces cell viability by dose- and time-dependent manner. Furthermore, high lignin concentrations induced apoptotic cell death in hMSCs. Our result indicated that lignin derived from B. flabellifer biomass has high antioxidant activity with moderate toxicity, suggesting its utility in biological applications.