In Ghana and other countries pursuing elimination of lymphatic filariasis (LF), suspect cases of lymphoedema and hydrocele are routinely enumerated by community health workers (CHWs) during mass drug administration (MDA). These data, in addition to cases captured through the routine out-patient department are used for burden estimation and health service planning. To date there has been no systematic evaluation of the reliability of these data in Ghana. In December 2022, we conducted a cross-sectional survey of LF morbidity in two evaluation units in the Upper West Region of Ghana, including 19,180 participants. Participants with swelling affecting the scrotum or limbs were examined by clinicians to confirm whether symptoms were due to LF. Participants were asked whether their household had been visited by a CHW during the previous MDA. Suspect cases were asked whether they had reported their condition to a CHW or sought care elsewhere. We estimated the prevalence of each condition according to survey data and pre-existing routine data collected by CHWs and compared estimates. Lymphoedema prevalence rates were 87.3 and 61.2 per 10,000 in the two evaluation units, and hydrocele prevalence rates were 111.3 and 65.3 per 10,000 males. Routine enumeration underestimated lymphoedema prevalence by 81% in both cases, and underestimated hydrocele prevalence by 41%–52%. Nearly all households were visited during the previous MDA, but only 60.7% of lymphoedema and 28.3% of hydrocele cases had reported symptoms. 61.8% of lymphoedema and 42.9% of hydrocele cases had sought care from health facilities. Routine surveillance underestimates the prevalence of LF morbidity in the study area. Process modifications, including re-training of CHWs and health workers should be considered to improve data for service planning and validation of LF elimination. Anticipating cessation of MDA, continuous health service delivery, with periodic coverage evaluation, should be prioritised to strengthen passive surveillance.