We present the second NuSTAR and XMM-Newton extragalactic survey of the JWST north ecliptic pole (NEP) time-domain field (TDF). The first NuSTAR NEP-TDF survey had 681 ks total exposure time executed in NuSTAR cycle 5 in 2019 and 2020. This second survey, acquired from 2020 to 2022 in cycle 6, adds 880 ks of NuSTAR exposure time. The overall NuSTAR NEP-TDF survey is the most sensitive NuSTAR extragalactic survey to date, and a total of 60 sources were detected above the 95% reliability threshold. We constrain the hard X-ray number counts,
log
N
–
log
S
, down to 1.7 × 10−14 erg cm−2 s−1 at 8–24 keV and detect an excess of hard X-ray sources at the faint end. About 47% of the NuSTAR-detected sources are heavily obscured (N
H > 1023 cm−2), and
18
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8
+
20
% of the NuSTAR-detected sources are Compton-thick (N
H > 1024 cm−2). These fractions are consistent with those measured in other NuSTAR surveys. Four sources presented >2σ variability in the 3 yr survey. In addition to NuSTAR, a total of 62 ks of XMM-Newton observations were taken during NuSTAR cycle 6. The XMM-Newton observations provide soft X-ray (0.5–10 keV) coverage in the same field and enable more robust identification of the visible and infrared counterparts of the NuSTAR-detected sources. A total of 286 soft X-ray sources were detected, out of which 214 XMM-Newton sources have secure counterparts from multiwavelength catalogs.