This prospective study investigated the frequency and intensity of postoperative pain and identified associated factors in adolescents undergoing two-visit root canal therapy. Sixty-four patients aged 11 to 18 years old presenting with molars with pulp necrosis were assigned consecutively to two visits (plus an interappointment dressing using calcium-hydroxide paste). Pain intensity was recorded on a visual analogue scale (VAS) of 0-5. Data were analysed using multivariate logistic regression. The frequency of postoperative pain was 32.8% (21/64), with intensities of VAS 1 and VAS 2 in 81%, VAS 3 in 14.3% and VAS 4 in 4.7% of the 21 cases in which it was experienced. Spontaneous preoperative pain (odds ratio (OR) = 6.60; 95% confidence interval (CI) = 1.61-26.97; P = 0.009) and absence of apical perodontitis (OR = 5.65; 95% CI = 1.34-23.87; P = 0.01) were associated with postoperative pain. The frequency of postoperative pain was high, but the intensity, in general, was low, including flare-ups. The presence of spontaneous preoperative pain and absence of apical periodontitis increase the probability of suffering from postoperative pain.