The issue started to become apparent in the early hours before spiking at around 8 a.m. (ET); by noon, the banking service still wasn't back to full operations.
Some customers also reported the issue was impacting credit cards. Instead, transactions were declined.
Wells Fargo blames the technical issues on smoke at an unspecified data center. In January 2018, the company experienced a glitch with customers reporting their bank accounts drained and others of multiple processed payments.
The company later said it is working to fix the "intermittent" outages in a second tweet.
Wells Fargo customers found they couldn't access their online bank accounts Thursday, nor could they withdraw money from Wells Fargo ATMs.
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Thursday's apology echoed the one the bank issued last Friday, when its online banking and mobile app went down on a payday, preventing some customers from paying bills or accessing their accounts.
Dozens of comments posted beneath the announcement demanded answers and additional information.
Users took to Twitter to report the outage.
Later, the company cited the incident at the facility as the wellspring for the shutdown, noting that they are "working to restore services as soon as possible".