The vulnerabilities of global navigation satellite systems (GNSS) to signal interference have increased the demand for complementary positioning, navigation, and timing (PNT) systems. To address this, South Korea has decided to deploy an enhanced long-range navigation (eLoran) system as a complementary PNT solution. Similar to GNSS, eLoran provides highly accurate timing information, which is essential for applications such as telecommunications, financial systems, and power distribution. However, the primary sources of error for GNSS and eLoran differ. For eLoran, the main source of error is signal propagation delay over land, known as the additional secondary factor (ASF). This delay, influenced by ground conductivity and weather conditions along the signal path, is challenging to predict and mitigate. In this paper, we measure the time difference (TD) between GPS and eLoran using a time interval counter and analyze the correlations between eLoran/GPS TD and eleven meteorological factors. Accurate estimation of eLoran/GPS TD could enable eLoran to achieve timing accuracy comparable to that of GPS. We propose two estimation models for eLoran/GPS TD and compare their performance with existing TD estimation methods. The proposed WLR-AGRNN model captures the linear relationships between meteorological factors and eLoran/GPS TD using weighted linear regression (WLR) and models nonlinear relationships between outputs from expert networks through an anisotropic general regression neural network (AGRNN). The model incorporates terrain elevation to appropriately weight meteorological data, as elevation influences signal propagation delay. Experimental results based on four months of data demonstrate that the WLR-AGRNN model outperforms other models, highlighting its effectiveness in improving eLoran/GPS TD estimation accuracy.