Lead-acid batteries have been in extensive use to provide energy backup in numerous industrial applications. These batteries have the advantages of proven technology, low cost, safety, and a simple battery management system. However, they suffer from low efficacy, lower life span in terms of discharge cycles, lower discharge rate, lower energy density, and lower depth of discharge. Li-Ion batteries with superior technological features overcome these limitations of lead-acid batteries. The technological advancements in Li-Ion batteries, along with rapid growth in e-mobility and Battery Energy Storage Systems (BESSs) for various applications, are driving Li-Ion battery prices down. Currently, Lead-acid batteries are extensively used in energy storage applications. Replacement of bulkier lead-acid batteries with compact Li-Ion battery modules in existing transport vessels would reduce battery footprint, thereby providing relatively more space for other cargo and equipment. Though compact Li-Ion modules would improve the speed and turnaround time of the vessels, the possibility of failure due to thermal runaway and hot spots also increases due to compact packaging. A new methodology for carrying out detailed thermal analysis was established, and an efficient cooling mechanism was developed. Additionally, space optimization of multiple Li-Ion battery packs was carried out in CFD to achieve energy requirements in limited enclosure dimensions.