Fetal heart rate (FHR) is an important characteristic in fetal well-being follow-up. It is classically estimated using the cardiotocogram (CTG) non-invasive reference technique. However, this latter presents some significant drawbacks. An alternative non-invasive solution based on the fetal phonocardiogram (fetal PCG) can be used. But most of proposed methods based on the PCG signal need to detect and to label the fetal cardiac S1 and S2 sounds, which may be a difficult task in certain conditions. Therefore, in this paper, we propose a new methodology for FHR estimation from fetal PCG with one single cardio-microphone and without the distinction constraint of heart sounds. The method is based on the non-negative matrix factorization (NMF) applied on the spectrogram of fetal PCG considered as a source-filter model. The proposed method provides satisfactory results on a preliminary dataset of abdominal PCG signals. When compared to the reference CTG, correlation on FHR estimations between PCG and CTG is around 90%.