Abstract Background Data collection is the most critical stage in any population health study and correctly implementing fieldwork enhances the quality of collected information. However, even the most carefully planned large-scale household surveys can encounter many context-specific issues. This paper reflected on our research team’s recent experience conducting surveys for a quasi-experimental evaluation of a reproductive health program in urban areas of Karachi, Pakistan. We aim to describe the issues encountered and lessons learned from this process, and present some potential solutions for conducting future household surveys in similar urban environments. Methods The study followed a three-stage random sampling design. Initially, a Geographical Information System (GIS) was used to construct the sampling frame with union council (UC) area mapping and cluster demarcation followed by random selection of clusters in the selected UCs within the intervention and control sites. The second stage involved a complete household listing in selected clusters and the final stage was a random sampling of households with eligible women. Result This paper describes the issues that were encountered including technical problems related to GIS demarcation of cluster boundaries and hand-held devices for computer assisted personal interviews (CAPI), household listing, interviewing respondents on sensitive topics and their expectations, and ensuring privacy during the survey. Conclusion This study identifies a number of unique barriers to conducting household surveys in Karachi and highlights some key lessons for survey research in urban settlements. GIS mapping technology is a cost-effective method for developing sampling frames in resource-constrained settings. Secondly, the strategy of interviewing women immediately after the cluster is listed may be applied to make it easier to re-locate selected respondents and to reduce loss-to-follow up. Understanding local norms and developing culturally appropriate strategies to build trust with communities may significantly improve survey participation. Researchers should hire experienced female enumerators and provide continuous training on best practices for interviewing women on sensitive reproductive health topics in urban communities.