Alternative lengthening of telomeres (ALT) is a telomerase-independent mechanism utilized by a subset of cancers to promote replicative immortality. The ALT mechanism is driven by increased replication stress and persistent DNA damage response signaling that leads to a homology-directed repair mechanism called break-induced telomere synthesis (BITS). In particular, ALT cells are hypersensitive to inhibition of ataxia telangiectasia Rad3-related (ATR), a DNA damage response kinase implicated in telomere mobility and recruitment of repair proteins for telomere elongation in ALT. However, little is known about what regulates ATR activity at ALT telomeres. Given the importance of ATR in the ALT mechanism, we hypothesized that known ATR activators, ETAA1 and TopBP1, regulate ALT activity and telomere synthesis. Here, we show that ETAA1 and TopBP1 localize to ALT telomeres at sites of ALT activity and telomeric damage. Furthermore, depletion of ETAA1 and TopBP1 leads to defects in ATR signaling, a decrease in BITS and compensatory engagement of telomeric MiDAS (spontaneous mitotic telomere synthesis) for replication stress resolution. Taken together, our findings show that both ETAA1 and TopBP1 are important for mediating BITS at ALT telomeres and may better inform our efforts in targeting the ATR signaling pathway in ALT-positive cancers.