An improved hydrogen generation system comprising: a hydrodesulfurization unit configured to desulfurize hydrocarbons and produce a process gas stream and a desulfurized fuel gas stream; a first pre-reformer configured to receive the process gas stream and convert heavy hydrocarbons within the process gas stream to methane to produce a pre-reformed process gas; a second pre-reformer configured to receive the desulfurized fuel gas stream and convert heavy hydrocarbons within the desulfurized fuel gas stream to carbon monoxide and hydrogen to produce a pre-reformed fuel gas stream; a first heat exchanger configure to dry the pre-reformed fuel gas stream by cooling the pre-reformed fuel gas to a temperature below the dew point of water producing a dry fuel gas stream; a second heat exchanger heating the dry fuel gas stream forming a heated dry fuel gas stream; a reformer having a combustion zone and a reaction zone, wherein the reaction zone is in fluid communication with the first pre-reformer and configured to receive the pre-reformed process gas originating from the first pre-reformer, wherein the combustion zone is in fluid communication with the second heat exchanger and configured to receive the heated dry fuel gas stream originating from the second heat exchanger, wherein the reformer is configured to produce a syngas stream within the reaction zone and a flue gas within the combustion zone in the presence of combustion oxidant; and a pressure swing adsorption unit configured to receive the syngas stream and produce a product hydrogen stream and a PSA off-gas stream, wherein the first pre-reformer is configured to operate at a first pressure and the second pre-reformer is configured to operate at a second pressure, wherein the first pressure is greater than the second pressure. a hydrodesulfurization unit configured to desulfurize hydrocarbons and produce a process gas stream and a desulfurized fuel gas stream; a first pre-reformer configured to receive the process gas stream and convert heavy hydrocarbons within the process gas stream to methane to produce a pre-reformed process gas; a second pre-reformer configured to receive the desulfurized fuel gas stream and convert heavy hydrocarbons within the desulfurized fuel gas stream to carbon monoxide and hydrogen to produce a pre-reformed fuel gas stream; a first heat exchanger configure to dry the pre-reformed fuel gas stream by cooling the pre-reformed fuel gas to a temperature below the dew point of water producing a dry fuel gas stream; a second heat exchanger heating the dry fuel gas stream forming a heated dry fuel gas stream; a reformer having a combustion zone and a reaction zone, wherein the reaction zone is in fluid communication with the first pre-reformer and configured to receive the pre-reformed process gas originating from the first pre-reformer, wherein the combustion zone is in fluid communication with the second heat exchanger and configured to receive the heated dry fuel gas stream originating from the second heat exchanger, wherein the reformer is configured to produce a syngas stream within the reaction zone and a flue gas within the combustion zone in the presence of combustion oxidant; and a pressure swing adsorption unit configured to receive the syngas stream and produce a product hydrogen stream and a PSA off-gas stream, wherein the first pre-reformer is configured to operate at a first pressure and the second pre-reformer is configured to operate at a second pressure, wherein the first pressure is greater than the second pressure.