Yes, you can only pay the 401(k) through a paper check. To meet Federal and State compliance requirements across all of our offerings, Intuit’s Direct Deposit service cannot be used to pay bills or make payments to individuals or entities who are not independent contractors or employees. 401(k) contributions to fidelity should go to the agency.
You'll need to check for third party applications that will enable you to pay 401(k) contribution to fidelity. You can also go directly into your bank and deposit the money to the receiver's bank account.
You can check these articles for more details about retirement plans and how QuickBooks keeps this record:
Just like paying any bill, such as heat and light, Fidelity surely has an online portal for you to electronically pay your liability and then record that payment in QuickBooks. Please consider this - there is not a single repository for your 401k contributions, nor even just 50 (as in states) - for QB to be able to directly pay to an account - especially when with multiple employees the employer liability has to be split over as many employees times 2 (employer and employee share MUST be separate in the fund itself) they would have to have a relationship with each and every fund out there.
Once you have your online setup at Fidelity it will probably take you less Thanh 2 minutes overall of your time to both pay into your company fund and record the liability payment inside QB