<p><i>Chlamydia trachomatis</i> (CT) infections in children present distinct diagnostic challenges, ranging from perinatal conjunctivitis and pneumonia to trachoma and, in older children, sexually transmitted infections. This review systematically evaluates contemporary laboratory methods for detecting CT in children. The methods are categorized by their distinct targets, beginning with morphological identification via stains (e.g., Giemsa, immunofluorescence) with or without culture; followed by immunological detection of antigens or antibodies (e.g., ELISA); and finally, molecular analysis using NAATs for DNA or RT-PCR for RNA. Each technique is rigorously examined based on analytical sensitivity, specificity, turnaround time, and technical requirements, with particular emphasis on age-specific specimen selection, sampling logistics, and ethical-legal considerations—especially in cases of suspected abuse. Our analysis confirms that NAATs, particularly real-time PCR, are the first-line diagnostic choice for their superior sensitivity in detecting asymptomatic and low-bacterial-load infections in children. RNA-based detection is highlighted as the preferred method for treatment monitoring due to its ability to differentiate viable pathogens. In resource-limited settings, rapid antigen tests offer a practical screening solution, though require NAAT confirmation. The review also discusses emerging technologies, including isothermal amplification and biosensors, for point-of-care (POC) testing. By synthesizing current evidence with pediatric-specific guidelines from the CDC, WHO, and European health authorities, this review aims to establish an evidence-based framework to guide optimal test selection, improve early detection, and inform public health strategies to reduce the CT disease burden in children.</p>