An intelligent transportation system in a metropolitan area is dynamic and prone to many external and internal attacks. These attacks result into modification, controlling, accessing, and altering private and public information of transport depots and their communicating agents. In this article, we have proposed a novel agent pseudonymous authentication with a conditional privacy preservation scheme in a metropolitan area. The proposed scheme utilizes identity-based encryption and a Boneh-Lynn-Shacham signature scheme for authentication, pseudonyms based for privacy preservation, and public key cryptography for pseudonyms generation. It achieves privacy preservation of depot's information. The primary objective of the proposed scheme is to protect privacy of communicating agents of transport depots during exchange of information (such as surplus and deficit vehicles and vehicles dispatch allocation and revocation). The proposed scheme is capable of avoiding the presence of impersonate genuine and malicious agents at transport depot. The proposed scheme uses an emergent intelligence technique for collecting, sharing, and analyzing transportation information. In addition, it also takes dynamic decisions for protecting privacy of transport depot's communicating agents. In this article, first, formal security proofs of the proposed scheme has been carried out using ProVerif tool, and second, Crypto++ package is used for the experimental and performance analysis. The experimental results reveal that the proposed scheme efficiently preserves privacy of transport depots' communicating agents.