Background Drugs used during pregnancy can adversely affect the health and life of the mother and unborn child. However, the fact that drugs are needed to mitigate complications during pregnancy cannot be avoided. The present study was designed to identify the common complications during pregnancy and assess the medications that have been used to mitigate those complications in an attempt to improve drug prescribing during pregnancy. Methods A hospital based cross sectional study was conducted at Manipal Teaching Hospital, Nepal in 275 pregnant women presenting with at least one complication and the drugs prescribed for the management of those complications were analyzed. Results Majority of the patients in this study were in the age group 20–24 (44 %) and in the third trimester (53.8 %). Maximum patients complained pain (back, abdominal, lower abdominal, neck, pelvic) as primary complication (24.3 %) which was followed by nausea/vomiting, upper respiratory tract complications, acid reflux disease and others. Of the total prescriptions eighty six (86) did not have any medicines prescribed to the patients except multivitamins and nutritional supplements. The average drugs prescribed per patient was 2.78 in outpatient setting and 5.41 in in-patients. Ranitidine, hyoscine butylbromide, paracetamol were the most frequently prescribed medications. Antimicrobials comprised 12.8 % of total drugs prescribed and 18 % of total drugs were fixed dose combinations. Two hundred and thirty four (234) prescriptions out of 275 were prescribed by brand names. Most of the prescribed drugs were from FDA pregnancy category B and C. Conclusion The present finding showed that pregnant patients were prescribed medications almost only when necessary and those considered safe during pregnancy were chosen to a large extent. However, few teratogenic drugs (2.49 % of total drugs prescribed) were also found to be prescribed which might need further assessments. Electronic supplementary material The online version of this article (doi:10.1186/s12884-016-1068-8) contains supplementary material, which is available to authorized users.