The genus Campylobacter comprises members known to be a leading cause of foodborne gastrointestinal illness worldwide. A study was conducted to determine the epidemiology and antimicrobial resistance of Campylobacter in humans in Morogoro, Eastern Tanzania. Isolation of Campylobacter from stool specimens adopted the Cape Town protocol. Campylobacter isolates were preliminarily identified by conventional phenotypic tests and subsequently confirmed by matrix-assisted laser desorption/ionization–time-of-flight (MALDI-TOF) mass spectrometry and polymerase chain reaction. Antimicrobial resistance testing employed the disc diffusion method. A small proportion of the test isolates was also subjected to agar dilution method. Risk factors for human illness were determined in an unmatched case–control study. Thermophilic Campylobacter were isolated from 11.4% of the screened individuals (n = 1195). The agreement between PCR and MALDI-TOF was perfect (j = 1.0). Symptomatics and young individuals were infected with higher numbers than asymptomatic and adults, respectively. The majority (84.6%) of the isolates were C. jejuni and the remaining were C. coli. Isolates had highest resistance (95.6%) for colistin sulphate and lowest for ciprofloxacin (22.1%). The rates of resistance for other antibiotics (azithromycin, erythromycin, tetracycline, cephalothin, gentamycin, nalidixic acid, ampicillin, amoxycillin, norfloxacin, chloramphenicol) ranged from 44.1% to 89%. Comparison between disc diffusion and agar dilution methods indicated a good correlation, and the tests were in agreement to each other (j ≥ 0.75). Human illness was found to be associated with young age and consumption of chicken meat and pre-prepared salad. Our data indicate the presence of antibiotic-resistant thermophilic Campylobacter in humans in the study area. There is a need for routine investigation of the presence of the organisms in gastroenteritis aetiology, including determination of their antibiotic susceptibilities.