Pregnant women are particularly vulnerable to iodine deficiency. Considering the rural-urban disparities in nutritional status in Pakistan, this study aimed to assess regional influences on nutritional iodine status of pregnant women in Pakistan. Data were collected from 1246 pregnant women in all trimesters of pregnancy who visited antenatal clinics for routine checkups in five Khyber Pakhtunkhwa province districts. Information concerning iodized salt intake and knowledge of iodine deficiency disorders (IDD) was obtained through an interview questionnaire. Goiter and urinary iodine concentration (UIC) levels were assessed by the palpation method and Sandell-Kolthoff reaction, respectively. Logistic regression analysis was used to quantify associations between residence (rural-urban), pregnancy trimester, and previous pregnancy outcomes with knowledge about IDD, iodized salt intake, presence of goiter, and UIC <150 μg/L. Among study participants, 87.7% had no knowledge about IDD, and only 21.0% were consuming iodized salt. Goiter was present in 25.5% of the women. The median UIC level was 131 μg/L, and 41.3% of study participants had a UIC ≥150 μg/L. There were no significant differences between pregnant women from rural and urban settings in regions with a solid socioeconomic status with respect to knowledge about IDD, iodized salt intake, iodine deficiency, and goiter prevalence. Urban-rural differences were observed only in socioeconomically disadvantaged districts. Only pregnant women living in the Lakki Marwat district had higher odds of having knowledge of IDD and iodized salt intake than those from rural regions. Trimesters of pregnancy and previous pregnancy outcomes had no significant effect on the outcome measures. Relative to a national nutrition survey conducted in Pakistan in 2011, the results from this study indicate that UIC levels remained stable with mild iodine deficiency, whereas rates of goiter and iodized salt intake remained high and low, respectively, especially in rural areas. Rural-urban disparities were observed only in socioeconomically disadvantaged districts, and these disparities limit the effectiveness of the IDD prevention program in rural areas in Pakistan. Thus, implementation of mandatory salt iodization requires improvement, and program effectiveness should be continuously monitored to prevent adverse health effects of iodine deficiency during pregnancy.