We examined methane (CH4) variability over different regions of India and the surrounding oceans derived from thermal infrared (TIR) band observations (TIR CH4) by the Thermal and Near-infrared Sensor for carbon Observation—Fourier Transform Spectrometer (TANSO-FTS) onboard the Greenhouse gases Observation SATellite (GOSAT) for the period 2009–2014. This study attempts to understand the sensitivity of the vertical profile retrievals at different layers of the troposphere and lower stratosphere, on the basis of the averaging kernel (AK) functions and a priori assumptions, as applied to the simulated concentrations by the MIROC4.0-based Atmospheric Chemistry-Transport Model (MIROC4-ACTM). We stress that this is of particular importance when the satellite-derived products are analyzed using different ACTMs other than those used as retrieved a priori. A comparison of modeled and retrieved CH4 vertical profiles shows that the GOSAT/TANSO-FTS TIR instrument has sufficient sensitivity to provide critical information about the transport of CH4 from the top of the boundary layer to the upper troposphere. The mean mismatch between TIR CH4 and model is within 50 ppb, except for the altitude range above 150 hPa, where the sensitivity of TIR CH4 observations becomes very low. Convolved model profiles with TIR CH4 AK reduces the mismatch to less than the retrieval uncertainty. Distinct seasonal variations of CH4 have been observed near the atmospheric boundary layer (800 hPa), free troposphere (500 hPa), and upper troposphere (300 hPa) over the northern and southern regions of India, corresponding to the southwest monsoon (July–September) and post-monsoon (October–December) seasons. Analysis of the transport and emission contributions to CH4 suggests that the CH4 seasonal cycle over the Indian subcontinent is governed by both the heterogeneous distributions of surface emissions and the influence of the global monsoon divergent wind circulations. The major contrast between monsoon, and pre- and post-monsoon profiles of CH4 over Indian regions are noticed near the boundary layer heights, which is mainly caused by seasonal change in local emission strength with a peak during summer due to increased emissions from the paddy fields and wetlands. A strong difference between seasons in the middle and upper troposphere is caused by convective transport of the emission signals from the surface and redistribution in the monsoon anticyclone of upper troposphere. TIR CH4 observations provide additional information on CH4 in the region compared to what is known from in situ data and total-column (XCH4) measurements. Based on two emission sensitivity simulations compared to TIR CH4 observations, we suggest that the emissions of CH4 from the India region were 51.2 ± 4.6 Tg year−1 during the period 2009–2014. Our results suggest that improvements in the a priori profile shape in the upper troposphere and lower stratosphere (UT/LS) region would help better interpretation of CH4 cycling in the earth’s environment.