A pulpotomy is the therapy for management of pulp exposures due to caries in symptom-free primary molars. The aim was to longitudinally compare the relative effectiveness of the Er:YAG laser, calcium hydroxide and ferric sulphate techniques with dilute formocresol in retaining symptom-free molars. Two hundred primary molars in 107 healthy children were included and randomly allocated to one technique. The treated teeth were blindly reevaluated after 6, 12, 18, 24 and 36 months. Descriptive data analysis and logistic regression analysis accounting for multiple observations per patient by generalised estimating equation were used. Additionally, various influences including tooth type, upper and lower jaws, type of anaesthesia, operator and the final restoration on treatment success were evaluated (Wald chi-square test). After 36 months, the following total (considering clinical and clinically symptom-free radiographic failures) and clinical success rates were determined (in percent): Formocresol 72 (92), laser 73 (89), calcium hydroxide 46 (75), ferric sulphate 76 (97). No significant differences were detected between formocresol and any other technique after 36 months. However, the odds ratio of failure appeared to be three times higher for calcium hydroxide than for formocresol. No significant differences in total success rates were seen regarding the aforementioned influencing clinical parameters. The correct diagnosis of the pulpal status, bleeding control and the specific technique are highly important for long-term success of pulpotomies in primary molars. According to the presented long-term data, pulpotomies using ferric sulphate revealed the best treatment outcome among the used techniques, while calcium hydroxide resulted in the lowest success rates after 3 years. Therefore, we can recommend ferric sulphate for easy and successful treatment of primary molars with caries-exposed pulps.