(1) Background: Abnormal uterine contractility for nonpregnant women has been associated with gynecological pathologies and infertility. The objective of this study was to evaluate the ability of a novel monitoring technique to assess the contractility of the nongravid uterus using a simple, standardized, direct, in vivo methodology during the different phases of the menstrual cycle. (2) Methods: Twenty-six healthy women of reproductive age (28–48 years) were recruited. An ElectroUteroGraph (EUG) was used to measure the electrical activity from the contractility of the junctional zone endometrium (JZE) across the menstrual cycle. Derived recordings were separated into the early proliferative (EP) (n = 10), late proliferative (LP) (n = 31), early luteal (EL) (n = 27), and late luteal (LL) (n = 12) phases of the menstrual cycle. EUG recordings were performed by inserting a flexible electrode array into the endometrial cavity. (3) Results: Waveforms that were measured from the electrode closer to the fundus (1 cm distance) were processed. The Root-Mean-Square (RMS) Voltage Amplitude (VJZE-RMS) (in μV) and the Mean Frequency (fJZE-mean) (in cycles/min) of the JZE’s electrical activity, as direct indicators of the intensity and frequency changes in the JZE’s contractions, were extracted from the recorded waveforms. There was a trend in the median values of the VJZE-RMS decreasing from the EP to the LP phase (247–158 μV). During the EL phase, an upward trend was observed (158–374 μV, p < 0.05), reaching its highest value during the LL phase (374–477 μV, p < 0.05) when compared to the LP phase. The fJZE-mean showed the opposite trend, increasing from 2.5 cycles/min during the EP phase to 2.96 cycles/min during the LP phase. During the EL phase, a downward trend was observed (2.96–2.37 cycles/min), continuing to fall to 1.33 cycles/min, in the LL phase, with p < 0.05 when compared to the previous three phases. (4) Conclusions: The novel in vivo monitoring technique has shown clinically, for the first time, significant electrical activity differences in the different sub-phases of the menstrual cycle, recorded in a safe and painless way.