Background Neurological disorders are the most common cause of morbidity and mortality in developing countries. Available evidence on urban–rural differences on neurological diseases is scare in such countries. Our study objective was to determine the prevalence of neurological diseases in urban and rural tertiary care hospitals of Sindh, Pakistan. Methods This was a cross sectional study conducted in selected urban and rural region of tertiary care hospitals of Sindh, Pakistan. The outpatients medical records of adults (18 years and above) was obtained from January 1st, 2014 to December 31st, 2014. Results A total of 10,786 outpatients visit were recorded in this period. Mean age of the participants was 40.6 ± 15 years; majority was females 6104 (56.6%). About three-fourth of the patients were from rural hospital 7828 (72.6%). Common neurological diseases were headache disorders 3613 (33.4%), nerve and root lesion 2928 (27.1%), vascular diseases 1440 (13.3%), epilepsies 566 (5.2%), muscle disorders 424 (3.9%), psychiatric disorders 340 (3.1%) and CNS infection 303 (2.8%). Comparison between the urban and rural samples showed that ischaemic stroke (72.7% vs. 82%) and psychiatric disorders (2.1% vs. 3.5%) were more prevalent in rural area as compared to urban setting. Conclusion Stroke, headache and nerve and root lesion are major causes of neurological disorders in urban and rural settings of Sindh, Pakistan. The policy and planning must be focus on primary care, preventive measures and the promotion of health. Electronic supplementary material The online version of this article (10.1186/s12883-019-1424-1) contains supplementary material, which is available to authorized users.

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