Cross-laminated timber (CLT) has gained popularity worldwide in recent years, and its use in buildings and civil engineering structures has attracted attention in Japan. In this study, the life-cycle greenhouse gas (GHG) balance and costs associated with CLT floor slabs were evaluated with respect to small-scale bridge repair as the first instance of the use of CLT in civil engineering projects in Japan. Additionally, waterproofing treatment was applied to CLT slabs, and the potential GHG and cost reduction of CLT in comparison with reinforced concrete (RC) slabs were examined. GHG emissions were the smallest for non-waterproofed CLT slabs and the greatest for RC slabs. When replacing RC slabs with CLT slabs without waterproofing, fossil-derived GHG emissions can be reduced by 73 kg-CO2eq/m2 per slab, and fossil/wood-derived GHG emissions can be reduced by 67 kg-CO2eq/m2; however, the use of disposed CLT as fuel is essential. Moreover, a reduction in GHG emissions can be expected if RC slabs are replaced with CLT slabs that are waterproofed only once every 20 years. Further, the cost associated with RC slabs is 20% of that attributable to CLT slabs. Hence, measures need to be taken to reduce the cost of CLT and waterproofing materials.