Externally post-tensioned tendons can cause an initial compressive stress in steel–concrete composite sections at the hogging moment region, and then a part of the tensile stress in the concrete flange can be relieved. This study presents a detailed finite element analysis of the nonlinear flexural response of continuous steel–concrete composite beams strengthened with externally post-tensioned tendons. The initial post-tensioning force is introduced as an initial strain in the truss element that used to simulate the external tendons. The accuracy of the finite element model is validated using existing experimental works. The effects of tendon eccentricity, longitudinal steel rebar ratio, and initial post-tensioning force on the beam behavior are explored. Furthermore, deterministic and stochastic shrinkage effects are carried out to obtain the long-term random responses of the strengthened beams as well as unstrengthened beams. However, the ultimate capacity of the strengthened beam increases only by 8%, the cracked moment redoubles, and an affirmative behavior over the unstrengthened beams is obtained. Also, a rapid decay in the long-term deformation of continuous steel–concrete composite beams is obtained at the early age while a linear decrease in the remaining part of the age occurs.