The fast development of quantum computing presents a major challenge to classical public-key cryptographic systems and especially the Elliptic Curve Cryptography (ECC) which is based on the hardness of the elliptic curve discrete logarithm problem. This paper provides a comparative study of isogeny-based cryptographic protocols with ECC-based schemes of post-quantum secure applications. A SIKE-like protocol is adopted and used to test isogeny-based mechanisms under real-world conditions, in addition to typical ECC protocols. The comparison is based on the size of key, complexity of computation, use of memory and communication latency. Experimental results show that, whereas ECC is more efficient and has lower latency in a classical setting, isogeny-based schemes have a higher resistance to quantum attacks, but with a higher computational cost. The findings show a performance-quantum security trade-off, thus requiring to design optimized hybrid cryptographic frameworks in the future to support a secure communication system.