Low-carbon transport system is desired for sustainable cities. The study aims to compare carbon footprint of two transportation modes in campus transit, bus and bike-share systems, using life-cycle assessment (LCA). A case study was conducted for the four-campus (College Ave, Cook/Douglass, Busch, Livingston) transit system at Rutgers University (New Brunswick, NJ). The life-cycle of two systems were disaggregated into four stages, namely, raw material acquisition and manufacture, transportation, operation and maintenance, and end-of-life. Three uncertain factors—fossil fuel type, number of bikes provided, and bus ridership—were set as variables for sensitivity analysis. Normalization method was used in two impact categories to analyze and compare environmental impacts. The results show that the majority of CO2 emission and energy consumption comes from the raw material stage (extraction and upstream production) of the bike-share system and the operation stage of the campus bus system. The CO2 emission and energy consumption of the current campus bus system are 46 and 13 times of that of the proposed bike-share system, respectively. Three uncertain factors can influence the results: (1) biodiesel can significantly reduce CO2 emission and energy consumption of the current campus bus system; (2) the increased number of bikes increases CO2 emission of the bike-share system; (3) the increase of bus ridership may result in similar impact between two systems. Finally, an alternative hybrid transit system is proposed that uses campus buses to connect four campuses and creates a bike-share system to satisfy travel demands within each campus. The hybrid system reaches the most environmentally friendly state when 70% passenger-miles provided by campus bus and 30% by bike-share system. Further research is needed to consider the uncertainty of biking behavior and travel choice in LCA. Applicable recommendations include increasing ridership of campus buses and building a bike-share in campus to support the current campus bus system. Other strategies such as increasing parking fees and improving biking environment can also be implemented to reduce automobile usage and encourage biking behavior.