Diffuse optical tomography (DOT) is a new emerging modality in the diagnosis of soft tissue abnormalities. DOT image quality substantially depends on the reconstruction stage. In the literature, there are many reconstruction algorithms used in DOT systems. However, some algorithms were improved for solving specific cases but still need to be improved. The bi-conjugate gradient (BiCG) enhanced is one of the conjugate gradient (CG)-based reconstruction techniques for non-Hermitian systems. The BiCG provides a solution to a non-Hermitian system. However, it has erratic convergence in some cases. Therefore, DOT images reconstructed by BiCG can be at the wrong location and is inaccurate in some cases. In this study, we used continuous-wave diffuse optical tomography (CW-DOT) to acquire measurements from breast tissue phantoms with single or double inclusion at different depths and center-to-center separations and we have used the transpose free quasi minimal residual (TFQMR) reconstruction algorithm, improved as an alternative to BiCG for the first time in the CW-DOT system. Moreover, we have experimentally proved that TFQMR is superior to BiCG in some specific cases for the first time in CW-DOT. Therefore, we concluded that TFQMR has the potential to be able to be used in the reconstruction stage in CW-DOT.