Purpose Clinical features of acquired third, fourth, and sixth cranial nerve palsy showed variation among previous studies. Evaluation of natural course with objective criteria will establish accurate recovery rates and important factors for recovery. Methods Retrospective chart review was performed on 206 patients who visited a neuro-ophthalmic department with acquired third, fourth, and sixth nerve palsy. Aetiology and results of ocular exam on each visit were reviewed, and multivariate logistic regression analysis was performed to identify independent factors affecting recovery. Results The sixth cranial nerve was affected most frequently (n ¼ 108, 52.4%) and vascular disease (n ¼ 64, 31.1%) was the most common aetiology. Recovery was evaluated with change of deviation angle for 108 patients, who were first examined within a month of onset and followed up for at least 6 months. Ninety-two (85.2%) patients showed overall (at least partial) recovery and 73 (67.6%) showed complete recovery. In univariate analysis, initial deviation angle was found to be only significant factor associated with complete recovery (P ¼ 0.007) and most patients who experienced successful management of treatable underlying disease showed recovery. Conclusions With objective criteria based on deviation angle, overall recovery rate from the third, fourth, and sixth nerve palsy was 85.2%. Patients who had smaller initial eyeball deviation or successful management of treatable underlying disease had a high chance of recovery.