We report a new approach of reactive spinning to fabricate thermosetting cyanate ester micro-scale diameter fibers with aligned single walled carbon nanotubes (SWNTs). The composite fibers were produced by first dispersing the SWNTs (1 wt %) in cyanate ester (CE) via solvent blending, followed by pre-polymerization, spinning and then multiple-stage curing. The pre-polymerization, spinning and post-spinning cure temperatures were carefully controlled to achieve good spun crosslinked fibers. Both pristine and amino-functionalized SWNTs were used for the reinforced fiber spinning. Amino-functionalized SWNTs (f-SWNTs) were prepared by reacting acid-treated SWNTs with toluene 2,4-diisocyanate and then ethylenediamine (EDA). FTIR, optical microscopy and scanning electron microscopy (SEM) showed that the amino-functionalized SWNTs were covalently and uniformly dispersed into the cyanate ester matrix and aligned along the fiber axis. The alignment was further confirmed using polarized Raman spectroscopy. The composite fibers with aligned amino-functionalized SWNTs possess improved tensile properties with respect to neat CE fibers, showing 85, 140, and 420% increase in tensile strength, elongation and stress-strain curve area (i.e., toughness), respectively. NH2-functionalization of SWNTs improves their dispersibility, alignment and interfacial strength and hence tensile properties of composite spun fibers. Fiber spinning to align SWNTs using thermosetting resin is novel. Others have reported fiber spinning to align SWNTs in thermoplastics. However, thermosetting CE resins offer the advantages of low and controllable viscosity during spinning and reactivity with amino functional groups to enable f-SWNT/CE covalent bonding.