Web-based systems are vulnerable to security issues similar to any other applications. Due to the characteristics of web-based systems such as their distributable nature and cross platform accessibility, security challenges are predominant. Recently, more focus has been placed on how to handle security concerns in web systems. Current solutions to counteract the web-based system security challenges include web system languages, firewalls, Intrusion Detection Systems (IDS), Intrusion Prevention Systems (IPS), cryptographic techniques, digital certificates and signatures among others. However, attacks and threats such as cross site scripting (XSS), Distributed Denial of Service (DDoS), cross-site request forgery (CSRF) and structured query language (SQL) injection attacks are still common. This gives the impression that there are still security challenges in this regard, despite the efforts for detection and prevention of attacks. Consequently, due to their dynamism, secure architectures are pivotal for the security of web-based systems. The focus of this paper therefore, is to review the existing security challenges of web-based systems. It is evident from this literature study that most security challenges in web-based systems stem from the threat of unauthorized access and risks from implementing technologies and standards that are under developed as regards security.