To advance the technology of Certification by Analysis (CbA), as called for by the aerospace industry, the fatigue problems of SAE keyhole specimens are analyzed to demonstrate a subcase of CbA. First, phenomena identification and ranking table (PIRT) analysis is performed. Second, modeling of the key phenomena is conducted, and finally, verification and validation with the experimental results are achieved. In particular, the elastic/elastoplastic stress distributions in the keyhole specimens are obtained using the finite element method (FEM). Plasticity correction for stress/strain at the notch root is made using the modified Neuber's rule along with the Ramberg-Osgood equation. The low cycle fatigue (LCF) crack nucleation life is analytically predicted using the modified Tanaka-Mura model, a.k.a. the TMW model, given the material's elastic modulus, Poisson's ratio, Burgers vector, and surface energy, without the need for coupon fatigue data regression. The Tomkins equation is used to simulate plastic crack growth within the notch plastic zone. The above analytical life predictions are validated against the SAE keyhole specimen tests, becoming the first successful case of fatigue CbA at a sub-element level.