Carbon footprint (CF) analysis is widely used to quantify the greenhouse gas (GHG) emissions of a product during its life cycle. A number of protocols, such as Publicly Available Specification (PAS) 2050, GHG Protocol Product Standard (GHG Protocol), and ISO 14067 Carbon Footprint of Products (ISO 14067), have been developed for CF calculations. This study aims to compare the criteria and implications of the three protocols. The medium-density fiberboard (MDF) (functional unit: 1 m3) has been selected as a case study to illustrate this comparison. Different criteria, such as the life cycle stage included, cut-off criteria, biogenic carbon treatment, and other requirements, were discussed. A cradle-to-gate life cycle assessment (LCA) for MDF was conducted. The CF values were −667.75, −658.42, and 816.92 kg of carbon dioxide equivalent (CO2e) with PAS 2050, GHG protocol, and ISO 14067, respectively. The main reasons for the different results obtained were the application of different cut-off criteria, exclusion rules, and the treatment of carbon storage. A cradle-to-grave assessment (end-of-life scenarios: landfill and incineration) was also performed to identify opportunities for improving MDF production. A sensitivity analysis to assess the implications of different end-of-life disposals was conducted, indicating that landfill may be preferable from a GHG standpoint. The comparison of these three protocols provides insights for adopting appropriate methods to calculate GHG emissions for the MDF industry. A key finding is that for both LCA practitioners and policy-makers, PAS 2050 is preferentially recommended to assess the CF of MDF.