This paper presents measurements of $t\bar{t}$ production in association with additional $b$-jets in $pp$ collisions at the LHC at a centre-of-mass energy of 13 TeV. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 36.1 fb$^{-1}$. Fiducial cross-section measurements are performed in the dilepton and lepton-plus-jets $t\bar{t}$ decay channels. Results are presented at particle level in the form of inclusive cross-sections of $t\bar{t}$ final states with three and four $b$-jets as well as differential cross-sections as a function of global event properties and properties of $b$-jet pairs. The measured inclusive fiducial cross-sections generally exceed the $t\bar{t}b\bar{b}$ predictions from various next-to-leading-order matrix element calculations matched to a parton shower but are compatible within the total uncertainties. The experimental uncertainties are smaller than the uncertainties in the predictions. Comparisons of state-of-the-art theoretical predictions with the differential measurements are shown and good agreement with data is found for most of them.