Cotton (Gossypium spp.), a crucial cash crop in the United States, requires the constant monitoring of growth parameters for informed decision-making. Recently, forecasting models have gained prominence for predicting canopy indicators, aiding in-season planning and management decisions to optimize cotton production. This study employed unmanned aerial system (UAS) technology to collect canopy cover (CC) data from a 40-hectare cotton field in Driscoll, Texas, in 2020 and 2021. Long short-term memory (LSTM) models, trained using 2020 data, were subsequently applied to forecast the CC values for 2021. These models were compared with real-time auto-regressive integrated moving average (ARIMA) models to assess their effectiveness in predicting the CC values up to 14 days in advance, starting from the 28th day after crop emergence. The results showed that multiple-input multi-step output LSTM models achieved higher accuracy in predicting the in-season CC values during the early growth stages (up to the 56th day), with an average testing RMSE of 3.86, significantly lower than other single-input LSTM models. Conversely, when sufficient testing data are available, single-input stacked-LSTM models demonstrated precision in CC predictions for later stages, achieving an average RMSE of 3.06. These findings highlight the potential of LSTM models for in-season CC forecasting, facilitating effective management strategies in cotton production.