This study aims to quantify the perception of value and acceptance by citizens of the use of cyber-physical systems (CPS) in transportation systems and smart cities using neurotechnologies. The work has been developed in the main cities of the following Latin American countries: Spain, Ecuador, Colombia, and Argentina. Targeting urban, public transport-using graduates, it assesses CPS in smart cities and user experiences. Triangulating qualitative research and neurotechnology, the study extends the taxonomy of emotional domains. The results indicate that users do not always assign equivalent importance to what they truly feel, and it is noteworthy that the most important factor, both quantitatively and emotionally, is the application of CPS to improve efficiency in public transportation. The implications of these analyses are discussed in the final part of the article with the aim of providing recommendations to policymakers on the key aspects to be considered in the design and development of CPS for use in smart cities.