Objectives: Chlamydia trachomatis is globally reported as a pathogenic infection and is the most common bacterial cause of sexually transmitted infection (STI) in most countries. In addition, chlamydial cervicitis and the adverse complications of the first line treatment, namely, azithromycin failure are highly prevalent. Thus, the present study will be conducted to determine and compare the effects of single-dose azithromycin and its combination with moxifloxacin based on syndromic and etiologic methods in the diagnosis and treatment of chlamydial cervicitis. Materials and Methods: This is a study protocol for a randomized clinical trial which will be performed at the Women’s Clinics and Health Centers in Amol, Iran during 2018. Further, the study will evaluate women with cervicitis complaints, who have a proven case of chlamydial cervicitis through syndromic or etiologic diagnostic methods and meet the inclusion criteria for the study population. Discussion: To the best of our knowledge, this trial will be the first study to explore the effects of single-dose azithromycin in combination with moxifloxacin in the treatment of chlamydial cervicitis. The results of this trial will further reveal the diagnostic value of syndromic and etiologic methods in the diagnosis of chlamydial cervicitis.